I haven't read much of the Fantastic Four and barely remember those movies, but I agree that the x-movies left much to be desired in its handling of the women. Storm and Emma in particular (my personal favorite x-women) were shadows of their comic selves.
The problem with Lee-Romita Gwen wasn't that she didn't have any flaws, but that she lacked depth and consistency. Whatever flaws she had were momentarily used to stir up drama between her and Peter in a typical silver age fashion and then forgotten shortly afterwards.
Interestingly enough, what 616 Gwen and Emma's Gwen have in common is that they are predominantly plot-driven characters. The plot demands that 616 Gwen be the main love interest and more popular than Mary Jane so let's just borrow some characteristics from MJ, redesign the character, and ignore what came prior. The plot demands that Emma's Gwen be adored prior to her death so let's idealize the character and make her immediately supportive of Peter's vigilantism. With both characters you can see the strings behind the writing. (To be fair though, this is an issue that occurs repeatedly with several characters in the TASM films.)
Raimi's portrayal of Mary Jane certainly has its problems, but what she has in common with 616 MJ is that she is far more character-driven. Aside from seemingly always being in the wrong place at the wrong time, most everything about MJ from the character's occupation to her relationships with Peter, Harry, Flash, and John are a product of or influenced by insecurities brought about by an abusive childhood. That's good writing.
I never got that impression from watching the film, but I suppose I'm due for a rewatch.