I've already stated most of this in various threads of the rebellion forums, but I thought I might collect them here:
-Rebel improvements (1):
As you are aware rebels can't attack neutral worlds that are colonized, such as pirate bases. Apart from the Occupation planet that has already been fixed I have suggested something for the normal "neutral colonies": My base idea was to grant the Protev a new researchable ability which I called "Annexation". I thought it should be quite expensive and provide you the planet and maybe even it's structures and ships. KarlBar99 suggested then that instead this ability should let you take over neutral units and structures one by one for a fixed not-so-expensive price.
Right now I would suggest a combination of both. One ability that takes over a neutral planet, another ability that lets you take over neutral structures and ships, both with their own research and conditions. In order to take over neutral structures and ships you have to be in possesion of the gravitywell they reside in. This also means you can take over insurgent forces sent by enemy TEC players (not for free like the Rebel reinforcement abilites, though) to free up your gravity well.
The annexation ability that takes over a neutral planet would only give you the planet, but keep it's current hitpoints and population so it's less vulnearble to attacks right after being taken over.
-Rebel improvements (2):
While a great and strong ability the Rebel/Pirate reinforcements have a huge problem on larger maps: Collecting them from systems like large random multi is a major pain, especially when there are only two or three ships per gravitywell. A beacon like building, like the Vasari phase stablizer, would be neat. It could also be a beacon switch on starbases so they can call the Rebels (doesn't have to be purchasable, just a button in one of the free command slots would be fine - as long as autocast defaults to disabled).
If the reinforcements are not used on any beacon/starbase they "store up" to a certain amount (would be cool if this showed in the HUD somewehere), but only to a certain limit. Any unused reinforcements beyond that are lost to the player.
-Loyalist AI problem:
Loyalist AIs only build one starbase in their gravitywell. At least normal, hard and unfair ones do, but since the only major change is their income multiplyer this shouldn't be different on higher levels. Since the second starbase is one of the Loyalist strong points I think the AI should use it... well as effectively as an AI could use it.
-General suggestion, tactical slots for allied players:
It'd be great if players could somehow free up tactical slots for their allied players, either by sacrificing your own slots or by researching specific slots for allies in the planet upgrade menu. I would only make it available for full planets (no moons/asteroids/dead asteroids) and limit the number of slots to something around 6 to 8. I've always wanted to be able to extend my vasari phase stabilizers to non-vasari allies (without having to place a starbase there), and providing improved TEC repair platforms or one or two advent antimatter rechargers.
-General suggestion, new diplomatic missions for allied players:
Construct starbase at XYZ. Not originally my idea (calwyn12 stated it in response to my previous suggestion), but I like it. Asking a player to provide a starbase at my own planets, self-explanatory I guess.