Main differences?
My humble point of view:
Mechanics: basically the same, but since WoW has been the MMO with the most player base for several years, this is honestly not surprising at all. If something works, why not using it?
Story: I like SW:TOR story better, mainly because it has a story, that is centered (or at least gives the impression it is) on your character.
WoW never had a story that could be grasped by everyone, regardless of the lore knowledge.
Graphics: more or less the same, but I think SW:TOR could use a little bit more polishing on this side.
IP: they are way different, one is classic High-Fantasy; the other one is Sci-fi... not really much to compare on this.
PvP: the both need an awful lot of work on this side.
In two words: It depends
Personally I played WoW for several years, and it has changed from being a pretty hardcore game (vanilla) to easy-mode-we-like-nutella boys (Cataclysm);
SW:TOR feels new (mainly thanks to the different IP, obviously) and has a lot of space to improve.