His father not coming back in the series is the most baffling thing in your post, just due to how silly and pointless it is to include it in an already packed film.
Amuro finds him when they go to Side 6. He's there, crazy due to oxygen depravation and living in a garbage dump. He gives a piece of junk to Amuro as if it was a super upgrade to the Gundam, then Amuro leaves him there.
As they leave Side 6, the movie shows him crazed as he cheers the Gundam on in the battle that's being televised. He then falls down the stairs, presumably to his definite end.
It's just... So weird. I would understand it if at least this was the moment Amuro found out he's the one who "killed" his father. But he never does.
I'm still going to watch Zeta just because I want to see what else is there in the franchise and eventually get to Turn A, but this was a rough start.