I've played Eclipse three times now and I think all Dave's points are valid; though I don't quite agree with all of them.
The things I really like about the game are as follows:
1) clarity - the rulebook is excellent, and the mechanisms are all designed to show the information you need in the situations where they are relevant. The system of wealth versus earnings is very simple, but brilliantly executed. More games could learn from this;
2) for a 4X game, it's really quick;
3) there are tough decisions every turn;
4) the traitor mechanism: the last player to break a treaty loses 2VPs;
5) modifying your ships is cool. I can have tachyon drives on my cruisers;
6) the flow of play during the action rounds is quick.
The things I don't like are:
1) what the hell are you doing for the first five turns? All that happens is you explore and try to build your tech to a level where you can compete with the Ancients or with other players when you meet them. It's fine, but it drags a bit;
2) because of this for a 4X game, combat doesn't tend to happen until later. If you fight early, you've used actions you could have used to research, so you'll be sorry later;
3) the traitor mechanism - the last player to break a treaty can't form another until an opponent breaks a treaty and takes the card. Whilst I can kind of understand the reasoning, this is pure artifice;
4) hey, wait a minute - I've discovered Tachyon Drives. I've can put them in my fighters and my cruisers, but I have to WAIT to take another action before I put them in my big ships...? Unless I have nanotech, of course;
5) the system of discounts for tech has no relevance to the type of tech being researched - for example, computer types do not all fall within the same tech-type, therefore there is no benefit to researching a Positron Computer (+2 attack) then a Gluon Computer (+3 attack). This is counter-thematic, if not plain idiotic;
6) combat is slooooooooowwww;
7) the turn order mechanism is rubbish.
My thoughts on Dave's issues (you did ask, didn't you? No. Oh well - sit back anyway) are as follows:
Exploration: it could be argued that real-world empires don't all start on an even footing; nevertheless, games are a construct. A little imbalance is fine with me, but I can see how one player's situation might be greatly disadvantageous. This is slightly mitigated by the fact that you have a some choice where you place - or whether you place your tile at all. It's an OK solution, but I think I'd prefer an open galaxy with a Settlers-type mechanism of placement to mitigate advantage. I'm not saying specifically a Settlers mechanism - just something that allows a bit more starting balance.
Technology: I agree that, given that actions are limited by cost, there is no reason to artificially limit the tech types by chit draw as no race will ever be able to research them all. This is another artifice because it feels like, rather than a directed research spend, these future 'advanced' civilisations are basically discovering new technologies by lottery. One solution, given that there is already a discount system in place, might be asymmetric technology costs for the different races to encourage diversification. In fact, this is a good idea. I claim this idea for a future 4X game that I'm now going to design (and Dave and others at the club can tell me what I'm doing well and what I"m doing badly).
Combat: I don't so much mind the initiative idea, but the combat just takes so long - and I think that the system of I-fight-you-first-then-you-then-you-then-the-ancients means that someone who has a huge fleet can be beaten by someone relatively weak because they've had their fleet mashed by all the previous combat. It should be simultaneous. As far as the mandatory combat for entering someone else's territory, even that of an ally - this has been a known mechanism since the first Sid Meier Civ. I didn't like it then and I don't like it now, but I think it's perfectly reasonable given it's now a convention, otherwise there might be very little combat in the game.
Reputation: this is a bit artificial too, but it's better than the chit-draw system that scores at the end of Louis XIV. At least you get to draw a number of tiles and keep one. This mitigates the randomness a little, and I quite like the fact that some of the scoring is hidden just to add that little frisson of tension. Of course, it could be argued that this is a way of ramping up tension which should be inherent in the playing of the game.