Some people complain about Battle.net 2.0 in StarCraft 2 saying that there are many features missing from Warcraft III, like for example 'clan support'. What are the main differences between these games (having only Battle.net in mind)?
Warcraft 3 had:
Clan Support, which meant that you could actually put your account in a clan and have it assigned certain ranks. It also included a custom chat room for your clan, where the clan leader had a shiny golden icon (Oh how I loved it) and could ban people from his village.
Automated tournaments. Basically every other day, there was a completely automated tournament, where you just had to win enough games in 2 hours to get placed into the playoffs and the play a normal elimination grid from there. There were special rewards for this, e.g. winning a game in the RO8 of the playoffs was actually worth 5 wins or something for your account, which helped you unlock some of the race portraits for your accounts faster.
In Warcraft 3, you could actually save multiplayer games in custom games and continue them later. This enabled everybody in tournaments, for example, to quickly save the game if it started lagging and continue it at a later point. In SC2, if it lags too hard and you disconnect, the game is basically gone and you're screwed.
You could create as many accounts as you wanted. Wether this was a good or a bad thing for the game shall not be discussed here, but it is something that you can't do in SC2.
You could freely switch around between all servers. A couple of clicks and you were playing on the Korean ladder.
These are the things that SC2 doesn't have, but there are other things which both games kinda have but which many players consider being better implemented in WC3:
In WC3, your account had a simple, server-wide identifiable level. When you earned a certain amount of experience (gained by winning games), you leveled up (you also lost experience when you lost games). The advantage of this was that you actually had a meaningful representation of your placement relative to other players in the ladder. Due to the league and division system it is not that way in SC2. I still remember the day when Grubby went to Korea and actually reached Level 60 (something that only very, very few players did before him).
Albeit it is possible to do the same thing in SC2 to a degree, WC3 had an official, more expansive browser-based stats-database for all accounts including a wide myriad of stats based on everything you could imagine. You could literally go to the website and see that your winning percentage against race x on map y was n% when you used a blade-master as the first hero, and k% when you used a farseer as the first hero.
As a bonus (it isn't WC3 so not what you asked for, but this is one of the most commonly requested features for BNet 2.0), in BW you could watch replays together with multiple people online. This feature is currently not available in Starcraft 2, but it wasn't in Warcraft 3 either.
These are just a couple of things, and I will keep adding things as I think of them.