The bloom is a bit off the rose now with Champions Online. I'm still enjoying it, but here are some things that are not so good.
Combat simplicity. Most of my fights are "turn on auto-attack, use self buff when it's off cooldown". Most powersets are a bit more interesting, and adding the necessary defensive abilities makes things a bit more interactive. But there's nothing like the complex DPS rotations of WotLK-era Warcraft mechanics. On the good side, there is some fun in positioning and tactical play.
Power selection and respecs. It's very exciting to choose your powers and customize your character. It's very frustrating if you decide you made a mistake. You can respec ("retcon"), but currently it's impossibly expensive to actually do. (It'd cost me about 20x the money I've made so far to undo my early choices). RIght now, choosing powers creates anxiety, not fun, and I'm starting to resent my gadgeteer for his weaknesses.
Experience tuning. People run out of quests to do. For example, the game feels like it is designed with two options to get through levels 5-15: Canada or Desert. But having completed all the missions available to me in Desert I've been sent to Millenium City, the next zone, to find the missions there are too hard at my level. I tried doubling back to Canada to fill in the gaps but perversely I'm too high level to pick up the missions there. My supergroup buddies tell me you pretty much have to alternate back and forth between the two zones to do every single mission to barely have enough experience, and even then you run out of things to do later and have to grind. If that's true it's a serious mistake. Self-inflicted, too, apparently it was much simpler to level up before they rebalanced things at launch.
Don't get me wrong, Champions is a lot of fun. The respec and experience problems are pretty easily fixed and I'm hopeful combat gets more interesting at higher levels. MMOs are so complex, so many factors have to be correct. What a balancing act!