Looking over my roster of 60s, I guess the one that I used the absolute least after leveling would be Marksman. In fact, I think I used him exactly once in CB, after building him specifically for that, due to not understanding how much his extra turn on A1 absolutely messes everything up. Couple that with the fact that I had a pretty stacked HE roster, and he was basically just immediately relegated to the vault.
In terms of who I spent the most resources on relative to how much I actually used them, though, I think there's no question that the answer is Narma. I brought her to 60 and fully booked her, because I thought I could make a one-key UNM team with double ME built around her extend. No matter how much I tried, though, I just couldn't make it work. She's now sitting in the vault collecting dust. I did use her for a few months before I got Helicath, but given the amount I spent on her, she definitely takes the prize. Though I don't know if I'd go quite so far as to say I regret building her - I did get some useful insights into how randomness plays out over large sample sizes.