Matchmaking as a whole
Inability to stop bots
It's time to start making TF3. The economy used to stop me from saying that, but it's completely and utterly destroyed. They say that updates are hard because of the spaghetti code, so they might as well just start fresh. Use that new source engine, and fix up that hitreg. No matter what they try, though, it probably will not live up to what TF2 was in its glory days.