First off I think it makes it easier to balance classes by removing auto-attack since some classes use it and some don't. With out auto-attack you can more directly compare ability to ability of non-similar classes.
...but that doesn't seem to be the primary reason SWTOR dropped auto-attack. Their reasons seem to lie more with combat animations, where abilities are animated to match the GCD or channel time, and don't have to worry about too many other animations causing interuptions, the primary source of which is auto-attack abilities.
I have not seen how GW2 handles the removal of auto-attack as I was never interested in the first one and I'm not sure if I'll be interested at all in the second one. What I have been following is Tera, which also removes auto attack in the manner that it is played more like an action or FPS type game, rather the normal style of MMOs which is to select a target and fire off abilities.
Auto-attack has not been much of a relevant ability since the original EQ. In EQ your auto-attack damage was the majority of your damage (for non-spell casters at least), and your special abilities were minor bonuses that were used in addition to them. In most games since then, auto-attack damage simply isn't a significant enough portion of your damage to really be included in the game, it's just an outdated carryover that most game companies hadn't considered removing when they were designing the game.