If anything, the biggest problem that I see with Civil War is how obviously right Cap is, and how obiously wrong Tony is. It's why I think Winter Soldier is far and away the best MCU film, and Civil War is only pretty good.
Everything established in the preceding films makes it clear that Cap A) has incontrovertible personal obligations to always help Bucky (his closest friend, who always stood up for him, and who's been brainwashed and is as such absolutely not guilty of what he was made to do) and B) is certainly and unquestionably right about government oversight over super-powered persons or items being just too dangerous to allow. (Whereas on the other hand, Cap has demonstrated his moral character again and again, making him about the best judge of what's right in the entire setting.)
The powerful governmental oversight organisation that previously existed was actually a front for literal Nazis, and almost conquered the world. The new oversight attempt is spearheaded by General Ross, who is demonstrably a dangerous criminal (and it's frankly insane he's not in prison). This is a no-brainer. In the wake of the SHIELD-is-HYDRA reveal, the pro-regulation position is simply untenable to any reasonable person.
Which hurts Civil War, because it could only work if both sides did have about equally reasonable points, and that's just... not the case. But the film tries to make it seem like they do.
Yeah and it's something reflected in the Comics as well.
Needless to say, when watching Civil War I was so overwhelmingly for the anti-Reg side in the MCU setting and for Captain America's POV. The portrayal of Captain America in the MCU as a strong moral force that you can trust was set up very well in the MCU and that obviously played into Civil War as well. But being only one film, it only scraped the surface of what could've been really good issues to explore and we never really know what the 'regulations' that would've been imposed actually were.
This was an inverse of the comics where the Pro-Registration Side IMHO had far stronger points, but acted like a bunch of authoritarian 'tards because Marvel was continuing to descend in its moral messaging and decay mode (like recruiting supervillains to hunt down registration heroes) and forcing metahumans into training camps and government service, not mere 'registration' and even ending up killing dudes like Bill Foster/Goliath and other nonsense which resulted in Norman Osborn somehow ending up in charge of SHIELD/HAMMER and Barack Hussein Obama ultimately helping save the day and revoking the Superhuman Registration Act... *coughs*
But I digress...