I see some good things, and some bad things.
Trading has been totally nerfed on genius/incredible. Except on rare occasions, you can't get squat in return for cash or trade goods. Trading techs leaves you at a severe disadvantage as well. There are a few techs that seem to have been flagged as 'low value' by the AI so that you can obtain them... but really, I could have gotten 'basic repair' by myself

. Couple this with the fact that the AI's still sling techs around with each other quite freely, and you're in a world of hurt.
That said, I don't have a real problem with that at the two levels above intelligent. It's *supposed* to be unfair there. Some people have complained that trading is seriously screwed up even at intelligent (where the playing field is supposed to be level), but I have no experience with that. Genius is still beatable, and Incredible is close to impossible (it'd probably be completely impossible if it weren't for one thing...). But that's how it should be. So I'll give a (weak) thumbs up to the trade changes on the 'unfair' levels (genius/incredible), with a thumbs down in reserve if those changes also occurred on the 'fair' levels.
The tactical AI is noticeably better. Transports often get escorted, and damaged ships pull off for repairs. You still see corvettes ram into your overlords every now and then, but hey, nothing's perfect. Thumbs up.
One thing no one else has mentioned that I really like is the new selection of diplomatic messages. I *think* these are new to 1.04, and they're pretty spiffy. For example, if you trade at a severe diplomatic disadvantage, your statement is something like "Um... we'd like to trade some stuff, or something". This kind of flavor adds a lot to my game experience. Thumbs up.
Metaverse scoring: BIG thumbs up. The single most relevant factor in determining your score now seems to be difficulty level, with an enormous bonus for beating the 'unfair' levels, and piddly scores for beating lower levels. And that is *definitely* the way it should be.
Culture: Before, planets would start flipping at the drop of a hat. Control a couple influence resources, flop down a party palace, and most of the galaxy would rush to your side in a domino effect. If you could make it to dreadnaughts, the game was over on pretty much any level because of this. Now, they'll still flip, but you have to actually work at it a little. Which is how it should be. Culture was fixed without being neutered. Thumbs up.
That's all that's really stood out to me. There was some other stuff on the list of changes, but this is what I noticed. I'm looking forward to that expansion pack.