Planetary invasions:
I can understand why they wipe out everyone. It's not because you trash the standing army that you hold the planet. A substantial part of the population might go into a resistance, making planetary invasions a very tedious undertaking. Starting over with a clean slate (except for those peeps you bribed into joining you) by slaying everyone is an option, especially since the troops you used are turned into taxpayers again. Essentially, if they succeed, they get what they conquered. Quite an incentive if you ask me.
The slower design of ships is remoured to have been addressed in the 1.2 version of the game. The reason it didn't design ships that fast was to save computing power, I believe. I don't think having the same weapon preference actually degrades the use of that weapon. It only makes it more tempting for others to research the correct defensive techs.
Trading planets requires the AI to value their worth which is notoriously difficult to do. After all, a computer can't think in a context like we, humans, do. Basically, this is what makes creating a good AI so hard: get it to understand what's a good idea and what's a bad one. The more open the game is in term of options the harder it gets.
Having said that, it *is* possible to get planets from the AI but only when you've cornered him militarily. It will give up land in exchange for its life. So, if you can make it clear that he'll only live if he gets on your good side, he'll swallow his pride and give you what you want. It isn't much of a trade, but hey, you get what you ask, right?
The rules for placing starbases has changed over the course of the patches and I don't know if the AI was adjusted to compensate for that. Earlier rules ensured no starbase could be built within X spaces of another starbase. In that respect, his spamming was a form of protection. Perhaps coding a re-evaluation every time the AI builds a starbase would prevent him from putting starbases so closeby. If an area is 'served' it wouldn't build more starbases there but would focus on expanding them.
The power of mining starbases depends to a great extent on your own tech level. Their effect can be telling but I haven't encountered a situation where there effects became overpowering. Surgical strikes become important, however. In the later game, starbases become fragile so I believe it balances out.
The reduced efficiency sounds nice at face value but it has the tendency to create a very murky mechanic for the players if the expenses stay the same. As it is now, more in translated into research/manufacturing points. If the exchange rate changes depending on the number of facilities, it gets difficult to keep track of. If both the costs go down as well as the points generated, it's fine by me. Besides, the game mechanics don't prohibit the forming of balanced planets (they don't encourage it too much either). A research center doesn't get better if there's another one already present. It only starts to matter when there are proportional bonusses present such as capitals.
As the patches come out, the AI is becoming more and more aware of 'macro-politics'. A recent addition was the aspect of fear. If you go about conquering other empires, the others might just see themselves next on the plate and gang up on you. I haven't experienced that yet but then again, I'm not really agressive.
Aside the galaxy not being tidy, it is also huge. Those terrain features you speak of are very, very rare. Granted, they could add some depth to the game but you have to keep in mind the AI again. Will it be able to handle terrain? Remember, the objective of Stardock is to have the AI play a challenging but fair game. Adding options and situations only makes it that much harder. I would like some terrain, though.
The UP could indeed be done in another way. Now, measures can easily be negated just because those in favour didn't guess the correct answer (like how many modules are we going to allow). Being able to work in two rounds would work wonders. First you get to see who votes what and then you get to make deals. There are several suggestions floating on the forum to influence the measure being voted on, either by electing a chairman or by consensus.
I like those ethical dilemmas too. I love that undead army one that seems to stack on each other. It feels as if you're evolving while playing the game. There are others like that but it has been a very long time since I've encountered those. The one thing I hold against those dilemma's is that it can't really deal with the condition that you'll do anything to win except hurt your own people. If you keep that condition you'll end up good, neutral or evil depending on the dilemmas at hand.
NLCs are considered to be overpowered by many out there. The order of alignments in terms of power is Neutral, Evil, Good (or so most seem to agree on). I have no opinion on that.
The combat viewer is one of my major eye-candy gripes. Large ships bob up and down as if headbanging on the latest Felix Da Housecat-tune and many ships bump into each other once they get to medium size. And don't get me started on the visuals of those weapons. The beams are just fine and the missiles are okay, though a bit slow, but those mass drivers!
When I think mass driver, I think lots of noise, shrapnel/slugs, impacts and tracers. Imagine my surprise when my cool battleship (Huge hull) headbanged his way over to the enemy opening up all guns and releasing...a score of green blobs that happily (and excruciatingly slowly) edged their way to the enemy, who proceeded to exploded well before any of the fudge arrived.