Think of anything you like in Startrek Online, Champions Online, the forums or anything surrounding Cryptic and its various services, technologies et al that you like and miss in other games.
I have started playing TOR recently, and there are two things that I already miss:
1) Cryptic's "Shard" system.
I vastly prefer this method over the many servers other games use. I don't want to be tied down to a single server. I don't know if people I want to play with will end up on the same server or not (especially if I only get to know them when I meet tham later).
Now, people may say that "One-Server-To-Rule-Them-All" leads to heavy instancing, but I don't see the problem. Even on these Servers, instancing can be needed if the population is too large.
2) Account and Character Manamagent
I really like the [CHARACTER_NAME]@[ACCOUNT_NAME] concept. It avoids name collision between players and ultimately gives you a lot more freedom in your name. Sure, you have that problem with your account name, but that name is not as important for immersion and verisimilitude than your character's name.
3) The Foundry
It's not perfect, but I wish more games had a feature like this (and at least with the range of options that Cryptic provides, even though I would like to see more).
4) Character Custimization
Cryptic really has a wide range of options and TOR is definitely lacking in that regard. I also ultimately prefer if items do not have to determine your looks. (I found Age of Conan also had an interesting approach to that, giving you two paper dolls - one to determine your character'S bonuses and all, and one to determine your looks. So "collecting" items for more visual options was possible, without forcing you into builds and bonuses you don't care about. But I think the CO or STO level of freedom is more interesting.)