I didn't read any of it, but from what I gathered it wasn't the idea of having a trained superhero force, it was the idea of forcing super humans to fight for the government whether they intended to fight crime or not, because of their abilities.
If it had only been registration, I would have agreed with Iron Man's side--government has a legitimate interest in knowing what, in its territory, can cause damage on the scale of superhumans--but the minute they started turning registration into the fascist glee club that is the Fifty State Initiative and detaining people over what are basically ideological differences, creating a system of indefinite incarceration for political prisoners, they lost the moral high ground--precipitously.
I won't say that Tony's methods weren't shit.
They were. But in the end I had to go with his side because of the benefits it offered. And I kinda feel like a bastard for saying this but since the superheroes had abilities that could be used to fight crime, why shouldn't they be drafted into service?
IIRC, Tony said the trans-dimensional prison holding superheroes who resisted registration was only a temporary thing, meant to demonstrate the strength of a prison that would
finally hold super-villains. One of his points was that it was getting ridiculous to have to keep putting sv's in jails that they kept breaking out of.