These are the 3 that are the most obvious for me:
1. The child is the Catalyst, the Catalyst is the Citadel, the Catalyst controls the reapers (therefore, the Citadel and the catalyst are the same "person" and this person controls the reapers) since that is the case, why didn't he just... open up the citadel relay in ME1 to let the reapers in? What is the point of having Sovereign try to activate the Citadel (which is the boy and the Catalyst) when... the Catalyst (the boy) could have simply... activated it? He, after all, IS the Citadel. This makes the last two games completely pointless.
2. The mass relays destroy entire sectors of the solar systems when they are destroyed, we know this because this is exactly what happened at the end of the last ME2 DLC. Since all the relays are destroyed, it would cause an IMMENSE amount of damage, the vast majority of organic life would die from these explosions (we know this, again, from the DLC) - therefore, the same result the reapers were ordered to do, happens, so the entire point of the ending to make a choice so that you save lives, is irrelevant considering when you destroyed the mass relays, it destroyed the vast majority of life (same thing the reapers wanted). - edit: didn't notice you already put this one on your list, good stuff.
3. One you mentioned already, but I will expand on it. The purpose of the reapers is to kill all synthetic life and kill all but a tiny fraction of organic life so that it can evolve - the purpose of this is because synthetic life tends (based on a theory only) to kill its makers in the cycles. Our "cycle" has the Geth, they are our synthetic enemy. Not 3 hours before the final battle, we made complete peace with the Geth, Not only that, they are helping us fight the reapers, who are in fact the only actual threat to organic life (thus making the entire ending a giant plot hole).
There are even more still, but I need to hit the sack.