Deus Ex
System Shock 2
Thief 1 and 2
While these games still excel in story, atmosphere and depth, there are quite a few things about them that could use an upgrade.
Graphics for one. Even for their time they were nothing special in the visual department. Take the excellent aesthetic style of Deus Ex: Human Revolution and apply something similar to the original. Same goes for System Shock 2. I rarely ever felt like I was on a spaceship, unlike say the Dead Space games. The steampunk in Thief 2 should feel even steampunkier. Back then graphical capabilities were severely limited by the engine and hardware, but that is no longer a big concern, so there is no excuse not to inject some artistic flair into those games.
Gameplay is second, though mostly for Deus Ex and System Shock 2. Things like augmentations, psi-powers and ui could use some streamlining (by which I don't mean simplifying) so they are more intuitive and convenient to use effectively. Their combat could use improvement as well with better enemy AI, more varied enemies and better designed combat situations.
