Alyssa Moy
Athena, Goddess of Widsom
Deadly Nightshade [Dr. Tilda Johnson]
Dr. Evelyn Necker
Dr. Kavita Rao
Lady Octopus [Carolyn Trainer]
Dr. Moira MacTaggert
Maya Hansen
Monica Rappaccini
Ruby Thursday [Dr. Thursday Rubinstein]
Sage [Tessa]
Starlight [Dr. Tania Belinsky]
Superia [Dr. Deidra Wentworth]
Thena the Eternal
the Witch [Dr. June Covington]
Ooh, this is a definite head-scratcher. I'd say it's probably between Alyssa Moy and Maya Hansen, based solely on their creations. As a side note, I think it would be great if Marvel actually had a woman in their frequently Amadeus Cho-referenced list of the smartest minds.
"When even one American - who has done nothing wrong - is forced by fear to shut his mind and close his mouth - then all Americans are in peril."- Harry S. Truman
OP, you listed Dr. Jean Grey, as a possible runner-up in the smarts department, but I do believe that she was only designated as a Doctor in the FOX Movie Universe. Please correct me if I'm wrong, but I do not believe she has accomplished this distinction in the Marvel 616 Universe.
To be fair she was only 24 when she died, it's quite difficult to get a doctorate by that age. In the movies she was presumably in her mid 30s to early 40s, and had the comic version lived to this age she would certainly have also earned the degree by then. It's sad really, Jean is supposed to have a very sharp intellect, which combined with her telepathic talents should easily make her one of the smartest people in the entire MU, but this is almost never highlighted in the comics themselves. An adult, fully Phoenix-powered Jean would have been an excellent addition to the New Avengers cast, especially since she is a far more logical successor to Xavier than Beast is. Oh well, that ship sailed long ago.
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