Upon re-watch, I found my feelings hadn't really changed. I really liked it, but found the clumsiness of the body swap and stealing a plane from the Smithsonian to be really glaring errors. I thought Wiig was outstanding in the role of Cheetah as well. It's not as good as the first one, but it's still pretty damn good in most respects.
I agree with both your points and your overall assessment. And both those points could have been fixed with a few lines of dialogue. The body Steve inhabited could have been discovered to have been recently deceased but Steve's resusitation of the body leaves the man alive after Steve leaves, adding a bit of weight to that final scene.
There could have been a line of dialogue as to why a fully functioning fueled plane is just waiting for them, and another couple of lines where Steve says he doesnt know how but he understands how to fly it. Magic? The man whose body he is in was a pilot?
Easy fixes for glaring problems.