Massive Planetary Overhaul:
Idea:
Create a large number of new planets and celestial other objects.
Create a slew of new planetary bonuses,
Purpose: add another aspect of exploration to the game.
Execution:
Planets:
First off, there would be types to the planets we already know (Terran Class A, B, C), A being mild (Terran A=decent planet) and C being extreme (Terran C=awesome planet [homeworld]), while B would be somewhere in between.
Volcanic exploration research would have 3 levels (one for each Class) and Arctic would have two as Class A’s would need no research to colonize.
Ocean world Class A have a small amount of land and are hard to populate but eventually bring in trade money; Class B’s have less land and get a boost to income for resorts; Class C’s have no land and you need to research "Marine Habitats" to colonize, though the research increases max population on all planets that have water; Type C’s are also harder to bombard because the population is under water.
Class C Desert worlds need the "Modular Habitats" to colonize, as do Class C Swamp, Forrest, Class A and B Jovian Wolds, and Class A, B, and C Barren worlds.
Ship graveyards with ships that friendly ships do not automatically fire upon or count toward ship experience when destroyed.
Abandoned planets with derelict ships, structures, and even star bases.
Derelict super star bases in "Dead space" or "Magnetic Cloud" areas; these would be expensive to repair, but count as a colonized planet; would also yield great benefits when explored (activating defense weaponry, free ships, money, etc.). These would also have a high population max and health.
A very rare planet that is an extremely powerful super weapon; heavily defended and needs to be fully explored to be used; will sound a "a rival empire has found an ancient weapon" or something when operational, removing the fog of war from the planet for rival nations.
Many other colonizable planets.
Certain Class D, E, F planets that are uncolonizable and dangerous, i.e. a volcanic world that spits lava into space, a gas giant with powerful winds, or a young star with dangerous heart and radiation.
Star alternatives: Ultra massive stars like red super-giants; tiny white dwarfs that regenerate antimatter and mess with strike craft and sensors; tiny black holes with massive gravity wells that destroy ships when shields deplete; pulsars that deal an incredibly large amount of AoE damage every 900 seconds; mass gravitational centers that are just immense gravity wells at the center of systems; nebula cores that posses a large number of capture-able extractors. Binary and trinary (if possible) stars with immense gravity wells.
I'm already working on these. Check out the Novus Universum Mod. It's not out yet but it's in the works. It's much bigger than what you propose. 
Research:
Most is outlined in the last bit, but there would also be some other stuff improving population and planetary health.
Already reworked in my mod.
Planet Exploration:
Many, many new exploration effects, including things like "found derelict ship" where you get a free ship or "credit/metal/crystal cache" where you get one time free resources.
Make exploration cheaper, but make 10-20 of them, depending on the size/type of the planet.
Figure out how to code it and I might just include it in my mod.
New Planetary Defense
Adds booby-traps to the planet research so that if another empire takes it over, population and planetary growth is severely hampered depending on how far it is researched.
Not do able due to the way planets work.
Modeling: mostly just new skins
Phase lane Upgrades
Idea:
Make it possible to improve phase lanes (travel speeds).
Add tolls
Purpose: make more interesting travel conditions in "civilized space."
Execution:
Speed increase:
Create another tactical structure with the opposite effect of the inhibiter (friendly ships: Phase Jump Drive Charge Up Rate: 50, 25, 10, 5%; travel speed +100, 200, 300, 400%; no antimatter usage)
Upgrades like the structures mentioned later in "Building Upgrades" for greater efficiency.
Tolls:
A toll system added where players can set a toll for the use of controlled phase lanes; e.g. if an enemy/neutral player’s ship pays the toll (a zero tactical slot/max count 1/low cost structure), your empires ships and defenses will not fire upon them. The enemy ships (mostly scout vessels) will have a pay toll option with an autocast if the player deems fit to pay tolls—they could also just risk traveling without paying.
Players would also have the ability to blacklist, charge more from, and exempt certain empires, i.e. ones with which they are at war and peace.
Tolls could even be a planetary research option.
Pirates would probably not pay tolls.
Modeling: the same as the stabilizer, just a modified skin; a small structure for tolls.
This is not possible unless you want to tell Ironclad to remake the game engine. Please do though. lol
Fleet Diversification (Frigates and Cruisers):
Idea: each ship in the three vanilla empires has two to four alternates with very similar models. Each of these ships is obviously a bit different than the other of its class and would emphasize a set of strengths while falling victim to some weaknesses.
Purpose: gives a player more control over the type of fleet they want to field (e.g. a player who likes raiding and fast attack would purchase variants of ships that have higher weapon damage but less armor.)
Execution:
Build Menus: where a player would normally click on a ship and have it added to the construction cue, they click and are brought to a submenu. In these submenus, they will be given the option to purchase the other variants of the ships once the proper research is purchased.
Research Tree: all ships would have their own string of research elements, whether sequenced (e.g. Cobalt Frigate 1/5, 2/5, etc.) or in a more tree like fashion (research the first and the four open and you choose which you want from there). The first one would make more sense and be smaller on the research tree, but would be inconvenient for players who prefer the variant that is last on the list; the second would be more ideal, but would take up a large amount of space on the research tree.
Models: for this all we would need is to have slightly different models, maybe have a different texture and slightly different shape; putting small rocket pods on each side of a Cobalt Frigate and change the texture a little, for instance.
There is a hard coded limit. It's again related to the game engine and the UI set up. Talk to Ironclad.
Building Upgrades (Mostly Logistics; Maybe Tactical)
Idea: notice how every building costs four logistics slots. This would bump everything down to one and give players the ability to upgrade structures in a similar manner to star bases.
Purpose:
Give players the ability to create more durable super-structures more capable of withstanding enemy attacks. Consolidate resources in a specific system, e.g.
Give players smashed into corner the ability build and research (albeit at high cost) without having to go up against those overpowered third party planets for logistics slots.
Execution:
A military research lab that counts as 3, having heavy defenses, a shield and small defensive weaponry; a civics research center that counts as 3 and boost the maximum planetary allegiance; a super research station that researches both military and civilian, giving bonuses to both.
Refineries that not only count as 2 or 3, but also refine at a better rate, improving overall
Super-culture towers capable of potentially making planets to enemy culture.
Ship factory superstructures capable of pumping out capital ships, cruisers, and frigates, 2, 3 and 4 at a time. They would also double as a hanger and have fighters, bombers, and dedicated frigates.
Super Trade Ports would not only increase trade income, but also boost tax income, buff population growth, and decrease planetary research costs.
Upgraded hangers capable of fielding large numbers of strike craft and produce them at faster rates. They would also have light frigates at max level.
Upgraded defense guns would simply have more firepower and better ROF.
Phase jump inhibiters would increas in effectiveness and damage ships on the way out, potentially destroying them if they were already weakened.
Repair stations would repair faster, in a larger area, affect shield and recharge antimatter, and give ships temporary buffs.
Mine upgrades would be addressed in the research tree.
Race unique structures would pretty much remain the same or be more effective at their purpose.
Models: Serious changes, e.g double and triple refineries, mega research station sizes, etc.
Again game engine constraints. I would love this. Replacing everything with starbase type might be fun. But talk to IC.
Purposed Capital Ship
Idea: Give each individual capital ship its own tech tree and each level would give you points to allocate to different abilities, i.e. Kol Battleship level 2 gets +X skill points towards everything from travel speed to weapon damage.
Purpose: Make capital ships more adaptable and unique player to player.
Execution: not sure how the tech tree would work, but would probably be either a popup, appear on the research menu under diplomacy (an individual tree for each ship), or like the space station upgrade menu.
Modeling: each ship would probably have to have a whole set of different models.
This would also require a game engine overhaul. Talk to IC.
Remove Asteroids:
Idea: Put the resources on the planet itself.
Purpose: less clutter.
Execution:
Add another menu item to the planet popup (planet health X/Y, population X/Y, Metal Mines X/Y, Crystal Mines X/Y)
Add research to military so that bombing the planet does not destroy mines, allowing another empire to capture them and not have to rebuild.
Exploring the planet (which becomes far more than two times) reveals more mines.
Modeling: nothing changes.
Though of but how would you destroy them without taking the planet like a surgical strike? Less clutter? The game isn't cluttered enough! lol Again, UI and game engine constraints. See IC.
Sub-idea:
Idea: keep the asteroids, but make them exhaustible resources.
Purpose: extra boost in economy.
Execution: add another menu item to the popup (planet health X/Y, resource remaining X/Y).
Modeling: asteroids go dead when resources are depleted.
This was tried out in the orginal beta. It doesn't work. Games last waaaaay longer that any exashtable resources can handle. Then it's no fun. They might as well be infinite. Or else Sins would be just like any other harvest and build game.
Grand Empires:
Idea: have those planets that already have third person empires have other options than simply annihilating them.
Purpose: allow you to diversify your empire, giving various advantages.
Execution:
Annihilation: the same as the current system; destroy everything and build from scratch. If they surrender, you simply ignore them.
Subjugate: you destroy their fleet and preserve the infrastructure, reaping economic benefits of increased taxing and production, but suffering incredibly low loyalty (they may revolt at any time). If they surrender, you assimilate the rest of their fleet into yours (but you never know if they might start a mutiny.)
Negotiate: send an envoy to negotiate peace initially or a military fleet large enough to cause them to surrender, reaping the benefits of high loyalty, having the empire protect its own planet with ships that do not count against your cap, and diversified (strengthened) culture, while suffering lower tax income.
The concept of having the pirates in your pocket and being able to send a fleet against an enemy without them knowing it is from you.
Modeling: Nothing much to do here.
Again... Game engine... 
Though awesome. There's something like this in Civ5.
Awesome stuff but alas they have been thought of (for the most part) and the game just doesn't cooperate.
