I'm not familiar with the 4e variants. I hated the 3E prestige class, which threw magical powers into the mix. The class is a great mundane character archetype.
I think "Assassin" could be a theme, since any class can get into the biz (and what are adventurers, if not the assassins of monsters?). However, I think there is room for two full-blown classes with a stealth/exploration focus.
Rather than assassin/rogue, I would like to see Thief and Spy.
The thief's focus: luck, stealth, traps and devices, magical dabbling (since there are so many magical obstacles out there), acrobatics (climbing, tumbling, escape artist). The PC can sneak into a room full of guards, pinch the keys and the wine off the table, and get out again without being seen. Fighting ability not as strong as the spy, but more options.
The spy's focus (James Bond, Emma Peel): fighting with dirty tricks, disguise (the most underused ability of 1e assassins), social skills. Skilled with most common weapons and many exotics, or maybe they have mastered a specific fighting style (judo chop!). The PC can infiltrate an enemy base and make almost everyone inside believe they belong. They might do some assassination in a pinch, but this is a hero archetype, not a paid killer archetype.
Sure, you can make a good case for rolling them into one class, but it should also be easy to come up with unique and interesting class abilities that make the thief and the spy distinctive in play. They'd have a lot of overlap in skill access, of course, but so do the rogue and the ranger.