I play on both platforms and the multi on PC isn't that bad. If you have a group of people you already know ready to play with, an easy way to bypass the Ubiserver problems is to get Hamachi and create a virtual LAN network. It tends to be more stable than most game servers. And it allows me to play System Shock 2 co-op, so major points for that.

Really tough for me to pick favorites but...

Hero: (Antihero) Garrett of the Thief series (I was going to say the Vault Dweller from the Fallout series but since you dictate basically everything about him/her, it's different for everyone who plays.) Awesome voice acting and dry, pragmatic attitude make him a winner for me, much like Sam Fisher but Garrett is the grandaddy of them all, as Thief was the first of it's kind.

Villain: I must concur with a previous post and say SHODAN. By far one of the most memorable game villains I've ever had the fortune of destroying (or did I?) due to stellar audio engineering and quality of the writing. Does her job extremely well as you almost don't want to end her at some points since it was just so effing rewarding to hear her taunt and/or praise you in her own way through out the game.

Just realized those are both Looking Glass games but what can I say. A golden era of games, they made. 

R.I.P. Looking Glass Studios

Can't wait for Bioshock.