A few things:
I totally agree that MoS should have just got a regular sequel. You'll get no argument out of me there. I've been saying for months and months that Batman should just sit on the shelf while Superman gets the spotlight for a change.
And you're right, in the more modern depictions of their relationship Batman has been given the edge more often than not. But the fact remains that he's a guy who throws Batarangs next to a guy who can toss things out of the atmosphere. The two of them together can very quickly become ridiculous if it's not handled carefully, and doing it in live action is completely uncharted territory. A lot of the GA is not used to seeing them together.
It's not my intention to come off greedy here. I was perfectly content with the trilogy and ready to take a break from Batman films. But this is happening whether I like it or not, and I still care about the character and want what's in his best interest if WB is going after my dollar here. This could potentially dictate the direction of Batman in cinema for the next decade or so...obviously myself and every hardcore Batman fan here has our eye on this.
Again, I'm not saying I want Batman to PWN Superman in this film and just dominate everything. IF Batman is to be Superman's major opponent in this film (like they are heavily implying), then he needs to be a worthy opponent. It's that simple. With kryptonite added to the mix, I don't see why this is such an inherently bad thing. If you're going to introduce a plot device like kryptonite, obviously it will need to be paid off at some point and we'll see Supes more vulnerable. One of the best scenes in Superman Returns is Lex's beatdown of Supes on the kryptonite-infused island. Him stabbing Supes in the back? So badass! If we can have a scene like that in a film, where that version of Lex wasn't even a physically imposing threat...would it really such a crime to have a kryptonite-wielding Batman trade some blows with Supes?
Quite frankly, after the very video-gamey sequence CG Kal and Zod fighting each other while destroying Metropolis...I'd LOVE to see some on the ground, hand to hand stuff between Cavill and ________. It's be visceral and a nice change of pace.
I'm not saying this has to get turned into another Bat-glory hour. I think this should ultimately be a Superman movie where Superman learns something and becomes the better for it (and Batman too...they should learn from each other). As "greedy" as you think it might be for a Bat-fan to have specific wants for this film, I think some Supes fans are coming off a little insecure about the whole "vs" aspect of the movie. If Batman has to cheat to level the playing field I don't see how it reflects badly on Superman if he manages to inflict some damage, especially when he doesn't have Batman's training as a fighter.
Lastly, I think Lex could still be a MAJOR player in this film. I think there could be an interesting hate-triangle of sorts between Bruce, Lex and Superman. Similar to the Batman/Dent/Joker triangle of TDK.