As for Wonder Woman, I never really believed she was on Superman and Batman's level of popularity and iconic image. She is definitely in the top 5 when it comes to DC superheroes but she is nowhere near them. I always felt the whole "Trinity" thing was a bit forced.
WW is, at least for me, more of an icon, like Superman, than a famous character, like Batman.
And I always find female superheroes kind of awkward. She definitely needs to loose the '50s panties.
It's pretty simple. Aquaman has the reputation of being a joke. Whether we like it or not, that's how most people see him. MM would be expensive and require the audience to buy another alien. If we go with the original seven, we'd have more "non-humans" than "real" humans. If you want the audience to care about the characters, that could be an issue.
And there's no comparing the popularity of those two against the other five. MM is easily the least well-known of the seven discussed.
Also, with Aquaman, one would have to acknowledge that there are huge cities of fish people with superpowers living in the ocean..
If the J'onn is used, they shouldn't have him being from Mars (even not-so-geeky people now know that mars is a barren rock and that we would have known for a long time, if there lived intelligent life there), but rather that he is from a distant solar system, and possibly crashed on mars after barely escaping his dying planet.
If Warner is clever, they could tie it in with the Curiosity rover (or a later expedition), and have him being uncovered from stasis, kind of like in the intro of the animated series, following up with an alien invasion by the things that killed J'onn's civilization. Then this could be the basis for the (2nd?) film.
I, however, believe only the core 5 should be present in the first movie, and that all but Batman should get an introductionary film before the JL film. Sadly, this doesn't seem to be happening, which I'm pretty sure will hurt the overall quality. Hawkeye and Black Widow worked out, since they are basially just extraordinary SHIELD agents, but quickly explaining WW or Flash like that.. And GL, depending on what they do with the 2011-movie.
And last; that idea about a retired Batman being the (supposed) villain seems rally interesting! I do, however, think it should not be connected to the Nolan-verse, which is pretty firmly grounded in realism. Would be really cool if they started the series with batman having been around for maybe 20 years, but been retired for 10 or so, and then force the four to work together against a common threat, before revealing who he is and joining them in the end