I don't see how Civil War undid the ending of Iron Man 3, at least if you're referring to Tony blowing up all his suits. It was AoU that magically gave Tony a bunch of new armours without any explanation. At least they mention Tony trashing all his suits in CW.
And seriously: I couldn't care less about IM3 anyway, and I doubt anyone would have preferred Tony's ending in the MCU to be the conclusion to IM3 rather than his heroic sacrifice and death. And I'll honestly say that CW was the movie that saved Tony for me as a character. I hated how obnoxious he was (even by his own standards) in AoU and how he really didn't seem to feel any guilt for creating a genocidal monster that nearly destroyed the world.
Let me respond to that in parts
1) IMO Civil War undoes the ending of IM3, because at the end of IM3 Tony blows up all his suits and looks like he's going to settle down with Pepper.
However in Civil War, during a heart to heart chat with Cap he reveals that he cannot stop being Iron Man, and doesn't want to ( which is why he and Pepper are on " a break").
Now I hated Iron Man 3 as a film, and equally loathed Pepper Potts as a character. I was hoping that speech in Civil War was the end of her.
2) IMO RDJ's performance in Civil War is his finest as Iron Man because we see behind the facade of Tony's ego - not in the ridiculous way he had panic attacks in IM3, but in a believable way that shows how conflicted he is and where it's clear he feels enormous guilt over Ultron, which is why he so easily agrees to the Sokovia accords.
I too had lost a lot of interest in Iron Man - because after having a transformative experience while captive in that cave, IM2 , M 3 and to some degree AoU have him turn back into the ******* he started of as, and it was getting old.
Then came Civil War, with a more nuanced version of Tony, played brilliantly by RDJ. Very similar to your reaction, Civil War made Iron Man interesting and compelling again for me.