@ ready man: researched items already do appear different. they have silver lineout and a little silver embellishment in the lower left corner. for not fullly completed icons it gives you the number/ level currently researched.
as for the list: great idea. I'm not sure, if it's not even doable over string file, after all, that one controls all the text in the game as far as I can determine. never seemed to work for me though.
as for the shield/ hull change ... what exactly do you wish to accomplish by it? I mean the only thing I can think of is that mitigation is applied to a larger percentage of total survivability, which in and by itself is not a bad thing. if you just want ships to go down faster ... well, there is fast mode, which should do that. other than that I am fine with the current dmg/ hp ratios.
the rebellion/ civil war idea is very nice, but I think it goes a little too far. what you would need is a) planets that go to 0 allegiance should not be destroyed, but be independant and thus recapturable and b ) you'd need a lot more factors to determine allegiance or rather change in allegiance (since that is tied to resource gain there has to be a maximum). otherwise there are just too few ways to combat the whole thing and it becomes way too mechanic. you can use local fleet strenth as a factors, but that is the only thing currently in that I can see adaptable to this purpose. and implementing so many changes would involve quite a bit of components imo.
homefleet: a tempting idea to go via a set of proposals with varying benefits and needing to convince your government to agree on it. nevertheless, the way to gain support does not make me happy and on the whole, the system you describe does not sound so much simpler than the other stuff. I mean characters, inventory, maps, parties, mana? that's a whole range of new elements and sounds a bit confusing. besides we are talking two different things: I was talking more of what type of government to have which has a drastic impact on various factos. I'd say we have more than enough real life examples to see that communist, fascist, democratic, monarchic, etc. regimes act quite differently in terms of military, freedom, markets, research, religion and more. so while I was discussing more what impact the government had on the nation as a whole, you were more assuming a set government and how it reaches a decision.
my whole point is, I would appreciate more empire wide decisions. the only area really where the whole empire is concerned is research (and, in its limited state, diplomacy). what do I want to do? which path do I want to take? more civilian, higher econmic output? more efficient military, larger military, more advanced ship type? the other decisions are planet based, though have some impact on the rest of the empire. where do I strenthen my defenses? where do attack? where do I place my labs and trade ports? where do I need a resupply and constraction base? but, as I said, decisions that affect all planets alike are fairly rare and I'd be happy with a few more of them.