I've seen badfic that tries to characterize a Sue as "intelligent and rational," usually showing no evidence of any such thing, and that downplays emotion and moral thinking as irrational and deplorable. The fic I'm thinking of had a not!harry Sue that rejected ideals of courage in order go to along with and even support Voldemort's regime, deeming it to be the safest and most rational choice for personal advancement. And then it wallowed in Edgy Sue gore and squick for a little while anyway. She also had many supposedly intelligent plans to gain power and wealth, most of which took place entirely offscreen and consisted of hiring other people to do the thinking for her. It usually falls under "Dark" or supposedly "Grey" Sues. I haven't seen enough of those types to necessarily justify a categorization. However, there are potentially interesting points to be made about the importance of depicting emotions well, the importance of writing a character so that they actually seem smart, and suchlike, as well as the usual dark!sue criticisms of "separate character morality from the message of the fic so as not to promote doing this awful stuff". It could also be that I haven't seen that many of them, as my badfic trawling is near-exclusively Wattpad and is mostly dark!fem!harry, dark!percy or fem!percy. So those are my thoughts. Make of their tangledness what you will!