Alliance probably win more pug BGs because it has bigger population and more raiding guilds then Horde, so more geared people queuing..
As far as premades go, it's kinda even nowadays, but Horde has more people to chose from for this even though it has lower population. Alliance has like 15 players total capable to play in good premades, if some of those aren't online, have to fill up with whatever. That's why Alliance premades without bad players never have a druid, warlock and a rogue, good players of those classes quit and log rarely. Often there isn't a warrior too, but there's still about 3 good ones logging in.. So yeah, it's almost always priests/paladins/mages/hunters and a warrior but not always.
TL;DR: Alliance probably wins more more PuGs cause more BiS geared PvE heros queueing / Premades kinda even atm, but Horde have wider panel of PvPers to chose from for their groups, even though their overall population is lower.