Over in the Superman forum, a discussion got going about writing the Trinity that touched on Wonder Woman, and I thought I'd bring that part of it over here. (Lets see if the quoting works cross-forum…)
My thoughts on this is that, yes, there is evidence that it's tricky to write Wonder Woman stories, but I'm not sure that's because Wonder Woman is tricky to write in and of herself.
First factor here is that I believe you can't discuss Wonder Woman without touching on feminist theory and that the comic is made in a patriarchal world. Marston did put his own peculiar brand of gender theory into the character and the stories he wrote. But nearly every other writer afterwards has been male, and I think that hindered the development and examination of Marston's views of gender for a long time. For given her origin story, Wonder Woman is tailor-made to examine gender roles.
Second is that Wonder Woman is working against patriarchal norms, and that's perhaps most shown in her love interest. Under those norms, a woman cannot be allowed to be stronger or more capable than her man. That blocked lots of avenues for exploring and establishing Steve Trevor as a love interest, and then Perez simply removed him from consideration (even as he set out to partially explore some other aspects of feminism with regards to Wonder Woman). These norms are arguably part of the cause for the frequent shipping with Superman. It is arguably only now, with the movie, that a workable model for Wonder Woman's love life has arrived.
Third, I'd argue that Wonder Woman has a clear message: love in the meaning of compassion. (Here, I'd argue that she is the opposite of Batman, who ostensibly is about justice but to me really is more about authority; hence the Hiketeia where their ideas of justice come in direct opposition to each other. The Hiketeia also makes for a nice comparison piece with the Brubaker's Catwoman story Joy Ride, even if Batman is less uptight there.)
Fourth, I believe one aspect why Wonder Woman has such a muddled history is that she brings too many toys to the writers. Dealing with her love life and her feminist themes probably went outside the comfort zone (and maybe competence) of a lot of her writers, and thus they moved on to other aspects of her, and there they could find a lot. All of Greek mythology. A hidden utopian society. But without a strong grasp of the center of her character, that could also make her a bystander in her own stories.