I completely agree with you. I absolutely loath any kind of vs threads, I find them the lowest possible and most deplorable form of a discussion topic on NB and I would rather see them disappear in all their forms of the face of NB for ever. VS threads disgust me. However that's just my personal opinion and for some reason many people like making them. Forbidding them is going to make a lot of people unhappy and those threads would regardless be made. Which means we would have to constantly infract, close and trash those threads with a lot of complaints as a result. So yeah that section will remain as it takes in a large portion of those threads. Of course there are still people making such threads in the other Naruto sections, but the amount is way lower and they can't even utter a rightful complaint when we trash those threads as they didn't bother posting it in the right section.
So as much as I hate those threads, that section remains right where it is.
And spam and flame wars? Well if characters originating from the exact same series, with other words the exact same universe/context or whatever you want to call it, meaning they are bound by the exact same rules and thus any disagreement between people originates from a different interpretation of the exact same things, already cause such spam and flame wars, imagine what happens when it considers two characters that are from two completely different contexts? That's a thousands times worse than any regular Naruto vs thread. Superman vs Goku makes Naruto vs Sasuke look like a discussion between two cute loli girl scouts talking about their favorite cookies.
Naruto vs threads between Naruto characters, even if those characters never met, can still in theory be held to a certain degree because everything we know about those characters originates from the exact same context. They are bound by the same rules. However crossovers are not bound by the same rules, they aren't bound by any rules and as a result nearly everything you know about those characters is void. It simply doesn't count. So it's impossible to even hold such discussions, but still people do it. How? They are twisting and distorting everything just so that it fits their own needs. Lets assume that genjutsu works on Luffy. Lets assume Naruto can see Ichigo. Yeah that's easy, but the reality of the situation is that you are making characters up in your head on the spot that do not exist anywhere. Those are not Naruto, Luffy or Ichigo, those are things you created yourself, but try to make it appear like they somehow exist somewhere as otherwise you have nothing to back up your own statements. In the end it comes down to the same principle of playing a game, but making the rules as you see fit while playing it. Making two non-existent characters and give them all the abilities you see fit isn't much different than a crossover.
There are no facts or arguments in discussions like these, people are interpreting everything extremely subjectively to fit their own opinions and because there isn't a common reference point -a shared context- to back up their supposed facts and arguments, they end up in a vicious cycle. The starting point of crossovers is non-existing and made up, while holding the discussions people are making everything up as they see fit and as a result these discussions lead to nowhere other than severe spam and flamewars. Making a thread where people can post anything they want like 'hopnbpougpsougdpsoup' has pretty much the same contents value as a crossover, only they are more sincere considering people acknowledge they are just writing random crap.
Everyone who does not understand this concept of 'context', which is the most fundamental aspect to hold andy kind of VS threads as everything originates from there, should not be participating in them as they simply do not know what they are talking about and because most crossovers do not have such a context, they are nothing more than eyesores filled with spam, thus forbidden.