I agree, the ending of ME1 is probably one of the best examples of - ridiculously powerful entity gets beaten by the mere mortals, and still making it "believable", and not bullshit jrpg power of friendship beating god shit.
Sovereign was cataclysmically arrogant and convinced of it's own superiority - so the fact that the normal plan had failed because of inferior beings pissed it off no end, then it had to spend thousands of years hiding from it's lessors trying to find a solution, eventually getting so desperate that it's only choice was to bum rush the citadel. But the desperate plan worked, it got inside the closed citadel and it's brainwashed tool was at the controls and only needs to press a couple buttons and it's won - when Shepard and co turn up, and at literally the last second fuck over its plan.
So now exposed - it doesn't get a second chance at this - desperate, and very very pissed off, deliberately puts itself in a venerable position by possessing Saren, because it still needs his body to push those buttons - but also because it really wants to fucking kill Shepard with it's bare hands.
Wow, the bad guy losing because of it's own negative traits - arrogance and rage - it's almost like there are rules for good story telling that Bioware have completely forgotten.