I used to play a lot online with chat programs, but I don't any more, and I'm not sure that I really want to go back to it. It has little to do with tools, and more to to with the players.
Trying to coordinate an online game is much more difficult than face-to-face. You have to recruit players that'll actually stick around for more than one or two sessions, high player turnover was always a problem for me, and the people I regularly gamed with who also DMed their own campaigns had similar problems.
You've got players coming to the game with their own assumptions about the game that may radically differ from everyone else, and that can ruin party cohesion. With face-to-face games, you can try to get a party set up that has a reason for working together, but with an online game it's a bit tougher unless you have a sessions set up just for character building. IME this resulted in PCs that had little reason to work together, and because you've got a lot of character motiviations going every which way, not everyone's going to get involved as they might want and I think it's a factor in turnover. Then as a DM, I don't know why the player is doing the things they're doing, which hurts group cohesion. I remember one player who'd tend to go off on his own which annoyed me at first, but after he sent me some useful information on his character's background and motivations it made more sense and I was able to work it in.
This is bad enough using just core rules in a published setting. It gets progressively worse if you want to use house rules in a homebrew. I tried this with my last online campaign, and in practice it turned out to be a disaster. Some of it was a bit too much reliance on railroadong as a DM on my part. However, some of it was trying to keep the house rules communicated with the players, which is more difficult when you do it by email or webpages. Players for some reason seem less invested in an online game and tend to place less effort into it.
The time it takes to type things out and roll the dice with lag thrown in slows a game down. As a result the campaign doesn't progress very quickly. This also contributed to the high turnover I think.
Some of the problems could I guess be lessened by good online tools, since chat gaming was less than stellar. But even then, I think some of the biggest problems would still remain, and the biggest is that players just don't seem as invested in an online campaign.