as you correctly said, the current quick start only gives you things that you would have got most of the time anyway. however, there is a fine difference between quick start and normal start and that is intel. by the time you get to decide between early military and early economc, you'd have scouted a couple of planets in a normal game and have determinded whether an enemy is very close, like 2 - 3 jumps or not. this is a crucial piece of information in a game, as it determines how much time you would have, if any, to take advantage of an early economic expansion.
with the advanced start, you have a lot of resources, but no information on your surroundings. I don't have a patent recipe to deal with this, but it depends on the type of game. in team games, you could split roles and then some could go for eco and others for military, but in 1 on 1s or ffas, I'd usually opt for early military. but it is more or less a shot in the dark.
the second thing, and related to it, is the early hw upgrade. not in all games, you'd instantly do that, as the crystal drain is quite drastic early on. so, yeah, normal and quick start are not quite the same, but they are pretty close and I think it's a good compromise to shorten the early phase without taking away too many decisions.
with a real 'advanced start' option that would be different. you might have instant access to more powerful frigates if you get some labs or you could alraedy colonise everything around you. you might not even have to chose between 'will I get that ice planet or do I go for lrm's/ carriers/ illums'. and trust me, that's quite an important decision and you will see it if you try to defend that ice world with a bunch of lights against a squad of illums. I'm not saying an advanced start is a bad idea. I can well imagine myself using it as an option from time to time. I'd say we should discuss it in more detail. what exaclty do you have in mind? hw plus two asteroids? any ships? any labs? how do you determine what you want and what not? or do you get the same every time like in the quick start option? do you start with any research? I invite you to put together a good and well rounded concept for this idea in more detail and I'll gladly look at it and give you my thoughts on it. the idea has premise, but without more detail, it's hard to tell the pro's and con's.
loading screens: hm, an incentive to get entrenchment. enticing, a good idea. still, for the most part, I think people would find it confusing. they would have to manuipulate the art with something like 'check out the features of our expansion pack'. then it could work.
upgrades: well, you can queue up a lot of other stuff and it instantly deductes the resources, even though it is not yet possible to build them. ships if you don't have the research, structures if you don't have the tactical capactiy, fighters if hangars are still under construction. it would just be nice to queue an upgrade for a starbase when there is a battle going on and you want to think of other things than 'hey, I need to keep an eye on that SB and make sure it gets the upgrades asap'. the team made such great work with reducing micro, this would only be another logical step.
I'm open to any suggestions with the phase jumping in the empire tree. I would not particularly advocate a second column, since that might clutter the screen too much. have have the empire tree be in categories and inside those you can scroll, but their positions remains unchanced. for example, one category for planets, stars, etc. another for your fleets and a third for phase jumping ships. I think of something like found in some internet pages where you manipulate just the part of the site that your mouse actually hovers over and not the entire page. for example, in this forum, the quick replay field in white at the bottom of the page. if you full it up completely, there is a scroll bar. and you can scroll inside your post field independently from the whole thread page. so, maybe you could scroll the other items in the empire tree indepedently from the planet list and as such there would not be so much jirking around if items get inserted somewhere else.
yeah, have a look at the map and the empires that the ai's control. if there are many asteroids and volcanic planets, chances are it will have enough metal already.