Lee. It's a cliché for a reason. He's currently caught in a weird phase of historic judgement between Lost Cause hagiography and liberal hatred and minimization of his abilities, but I think his record speaks pretty plainly. He replaced Johnston and spent a year absolutely pushing the North's shit in, made them run through like 4 commanders, rolled the dice on going in the North twice in what were "close run things". I also think how he composed himself end of war was the perfect encapsulation of the old Virginia gentry and a true moment of American statesmanship. (Grant as well, obviously).

McClellan. If there's someone truly due for a historic reassessment it's him. Hindsight is 20/20, all is settled now and narratives can be crafted, but I think in the heat of the moment, McClellan performed ably. It's fun to sit and say "Oh he was so timid", but outside of a true wild card in Lee in the Seven Days Battles, he was doing the right thing. Bull Run was less than a year hence, both sides were still green. He built a mighty army and respected the fact it also happened to be the only thing standing between Richmond and DC. When he was brought back in for the Maryland campaign, he shut down Lee outside of South Mountain and stalemated Antietam. He would be the only Union general to check Lee and the ANV until Meade.

I also have soft spots for Rosencrans, Thomas, Mosby and a few others.