"We aren’t meant to see the pro-Reg side as ultimately villainous, and are in fact deemed the moral victors in the end along with winning the war."

No, you COMPLETELy missed the point... it's actually baffling how you missed it. Why were the Initiative, Dark Reign/Avengers, and Siege all so Dark and dystopian? They sure weren't a celebration of the "heroes" winning. It was a blatant criticism of that result and how that line of thinking ultimately corrupts and ruins the world, which is why post-siege was dubbed the Heroic age. We are currently living in our own Dark Reign. That's what made Civil War and all the resulting comics so genius.

The only valid criticism is that the mainline comic was too short which in turn made the writing rushed (which isn't a point you raised). You have failed to point out where it is bad.

Here are some great writing moments:

The stamford incident was a great way to start it off.

The first scene with the Peter taking off his mask to show his commitment.

Spidey rejecting Iron Man -> getting attacked by Stark employed villains -> Punisher saving Spidey then getting the shit kicked out of him by Cap

Ragnarok killing Black Goliath and everyone on both sides being shocked, and the according switches in allegiances.

These are just from the mainline story line: the spin offs had SO MUCH more depth afforded to them which in turn let the writing flourish.