With regard to Urdnot Wrex's political power, the truth of the matter is he had next to none beyond being one of the few krogan leaders actually attempting something approaching reconstruction. The female clans don't answer to him - in fact, it's the other way around. ME3 explicitly establishes that Krogan males, including clan leaders, defer to the females in political matters.
Now, you remember the Clan Nakmor ambassador in ME2? Clan Nakmor's a fairly secretive and small clan, and their ambassador is only present to petition for alliance with Clan Urdnot if Wrex leads Urdnot. Fast-forward to ME:A and visit the krogan colony. The vast majority of named krogan? Are from Clan Nakmor. The krogan colony population? About 60% female.
It doesn't break the lore.
Can't speak for the Quarian issue, though, because I haven't progressed that far through the storyline yet.
Completionism. :P
EDIT: It's also worth noting that the default, non-imported save starts for ME2/3 assume what amounts to incompetence on Shepard's part. No side quests completed, no speech checks passed, meaning it stands to reason that as far as ME:A canon is concerned, Wrex was very much dead when the Arks left for Andromeda. It fits even better, because Clan Nakmor doesn't attempt to ally with Clan Urdnot if Wreav leads it, so it stands to reason that instead of signing on with Wrex to try and rebuild (because he's dead and Wreav is an idiot), Clan Nakmor bails to start over on their own terms in Andromeda.
EDIT 2: You know how the news bulletins in the Nexus make mention of beacons to communicate with the Milky Way going unanswered? Consider the first bit of my previous edit. I'm thinking that a low EMS destroy ending is ME:A's canon, and with 600+ years passing, nobody's going to be responding. In part, because this is a setting that has viable instant very-long-range communication via quantum entanglement. If nobody's answering, and you assume that people would've known to answer, the logical conclusion is that there's nobody around to answer.