I would probably fix Secret Invasion because the problem with it was the core series was all just the heroes fighting copies of themselves or their dead team mates in the Savage Land for most of the series while the tie ins actually expanded upon the actual invasion. I would fix it by really cutting down the time they spend in the Savage Land, make the core heroes actually participate in the main fight (which they don't actually do until the last issue or two) and I would actually have them lose in the end. The world would get captured and they would be forced to battle a Skrull occupation of Earth. Thats how I would do it.
I would also like to fix Civil war as it was terribly one sided in favor of the anti-registration people and it completely antagonized Tony Stark just because he was obeying the law. The core problem of Civil War was that the people, not the government, the people chose to make superheroes register and thus the anti-reg guys came off as assholes for going against the will of the people they swore to protect. I would make it so that the government were the ones who forced the registration act to go through and then you would have this situation where the heroes have to fight the government to protect themselves.
The governments whole thing would be that they see heroes as a threat and they want to basically make them all like Superman from TDknight Returns, their own puppets by forcing them to become their agents and revealing their identities to them through the registration act. You have this situation where some heroes side with Cap, Iron Man, Spidey, Daredevil,... fighting against the registration act and on the other side you have some people like SHIELD, Nick Fury, Black Widow, Hawkeye and those guys fighting to keep get them all under government control because they see them as a threat.
Those are the two stories I would fix if I could and how I would do it.