Although I pre-ordered EU4 (lured in by the free CK2 deal), I've only now begun my first try-out campaign, so I thought I'd add something to this thread.
I should point out that I've never played EU3, so I'm not aware which features were introduced for that.
I'm playing as Denmark and have reached the 1570s after starting at 1444. I'm still only learning how to play, therefore. I'll split the comparison into two parts, with three things that stand out initially that I think are better in EU4 than in FtG and three things that seem worse.
Better in EU4
1. The number of options available - In peace resolution, for example, it's great to have the option of forcing your enemy to cancel treaties, release nations, renounce claims, etc., instead of simply demanding provinces and/or money. I also like the number of buildings available and the way that building runs throughout the game instead of being restricted to a few isolated phases.
2. The restrictions on expansion and the military - Lots of people moan about these on the EU4 forum, but I think that the system is generally a good one. Although it's too easy to fabricate a claim in order to get a CB, you really have to be careful in order to avoid becoming the target of a coalition (which has already happened to me, although I managed to avoid attack). I also like the force limits and the need to replace outdated ships.
3. Technology - I much prefer the allocation of monarch points and choosing ideas to shifting a slider one place every ten years.
Worse in EU4
1. Combat - The AI here seems to be better, but who on earth had the idea of allowing units to reinforce automatically to full strength following casualties? It's especially strange to see your armies reinforcing during a seige in enemy territory when they should be losing strength from attrition. This whole thing feels so unrealistic. The shattered armies mechanic is also difficult to take seriously. In my opinion, these two factors are definitely the worst thing in the game.
2. Religious conversion - It seems ridiculously easy in EU4 to convert to Protestantism. You take a prestige hit, but it doesn't seem to affect you that much. Meanwhile, you get to keep your alliances with Catholic nations, albeit with a small opinion hit. In particular, it takes only about nine months to convert a province, with guaranteed success (as far as I can tell) and using a resource (a missionary) that would only be redundant otherwise. Meanwhile, the increased revolt risk during the conversion process can be completely removed with the harsh suppression option. I actually think that converting a province is a bit too difficult in FtG, but EU4 goes way too far in the opposite direction.
3. Instant Stability Improvement - You have to spend administrative points on this, of course, but it just seems so unnatural, at least to someone who is used to FtG.
Maybe I've posted this too soon. I'm unable to comment on colonisation, for example. You've probably also noticed that I tend to favour restrictions, which other people might not like. But I hope that this gives some idea of what to expect as an FtG player trying out EU4.
Overall, I expect that I will continue to play both games, as I like them both. What I'd really like is a combination with the better features of each one, but that's just a dream, I'm afraid.