Just my two cents here; I don't think the Collectors are gonna be the main baddies. If I were to say I'd say the Collectors were under a Reaper's control, perhaps even more than one, and were hired to capture, destroy or simple 'make vanish' entire human colonies. That way Reapers would learn more about humanity, which, coincidentally, were fundamental in destroying Sovereign. The Reapers would learn more about humanity, the Alliance, their ships, their weaknesses and so forth, just planning to deliver the finishing blow in Mass Effect 3. Of course there's still the flaw that the Alliance came fairly ad-hoc at the Citadel Battle and they probably won't have that advantage every time but hey, what do the Reapers know?
Of course this is all just wild imaginations but perhaps there'd be a hint of truth in here