The biggest problem I ever had with 2nd edition was managing all the people who wanted to play in my campaigns. I started playing in 1994, began DMing shortly after that, and at one point I was running three separate groups, in three separate campaigns, each playing at least once a week. It was glorious.
Nobody I ever played with ever had any issues with THAC0; it was a little counterintuitive, but if you could add, you could manage it OK. After a couple of times, everybody had it down. I do think that the DM had a much greater impact on the game in second edition that in third, and definitely more than in fourth. So much relied on the DM's ability to make stuff up on the fly.
A minor quibble was a lack of consistency; not only in the rules systems, but also in items and spells and such. But like everything else, the final call was up to the DM, and what the DM ruled went. As a DM, one advantage of the hodgepodge of rules systems is that you could make pretty much anything work.
When 3rd edition rolled around, it definitely made the game simpler. The universal mechanic used for all actions was great, and prestige classes were a great idea. I think the only concept out of 4th edition that I really liked was the idea of ritual spell spells. Some character concepts of mine from earlier editions would have landed much closer to my ideas if ritual spells had been an item earlier.
I tell you, though, I miss the greater degree of open-endedness of 2nd edition, and the fact that there wasn't am attempt to have rules in place to cover every possible development in the game. I liked that magical items could be kept very rare and mysterious without it crippling the game or the characters. I also think that balancing classes by the xp needed to level works better than trying to pretend that a fighter and a wizard of equal level will ever be at the same power point. The only way to make that work is to make all of the classes mechanically identical, which was the 4th edition approach.
I also vastly prefer the multiclassing approach of 2nd edition. Some character concepts make no sense as one-class-at-a-time advancement.