I dont agree with your first paragraph, no matter what people on the internet want you to believe gamers do not consist of JUST Ninty fans. that makes no sense. You can be a Ninty fan and a Sony fan and a MS fan all at once, so no the audience is not just Ninty fans, otherwise people wouldnt have been hyped for Snake as they were, hell he was more hyped than Mega Man. What is the creteria for "strong" presence? When was the last time Mega Man had a strong presence on Nintendo? Anywhere really? he's been multiplat for a while. As for Simon, my thing is he's such an old character that most people playing wont even know who he is, even in his own series he's not the most popular guy, that goes to Alucard. But i guess he cant show up since it would be no different than Snake.
I just said that the Smash audience is comprised of Nintendo fans, nothing about them being only that. You can indeed be a Metal Gear fan and a Nintendo one, they're not mutually exclusive. Still, how good are those odds when the franchise regularly ignores said platforms like the plague ? When even Xbox and PC get the games before them ? The lack of exposure makes it more unlikely to get fans there, and Konami/Kojima don't seem to have much intention to change that. They themselves seem to think the audience is not a good match for the franchise, so why should Nintendo/Sakurai feel differently ?
The criteria to choose these characters will always be arguable, but it would be ridiculous to argue that Snake is just as much tied to Nintendo platforms as Mega Man. Mega Man (classic) has appeared on at least 16 games by my count on Nintendo platforms, not counting late ports (anniversary collection, etc), and his first 7 main games (and Rockman and Forte) were originally on Nintendo platforms exclusively. That's a strong presence. The fact that 9 and 10 weren't exclusive doesn't matter as much here, because it was still there at the same time, unlike every new main Solid game. And he was very well received. I don't know where you got the idea that Snake was more hyped... That's not my impression.
Whether Simon is less popular than Alucard or not, I don't know, but I do know that he's fondly remembered by many Nintendo fans from his NES, GB and SNES appearances, and he has been on far more around as much or more games as Alucard. Either way, he would be the best rep for Castlevania on Smash, a franchise that has always being close to Nintendo platforms. Younger Nintendo fans might not know him as much, true, but at least he and his franchise is largely available for them on these platforms.
Again, I don't see why Snake should have priority over these characters when he has already been on Smash, barely appears on Nintendo platforms, and has closer ties with Sony ones. It should be obvious by now that many Nintendo fans would even react negatively to him being there again, the opposite of what you're trying to accomplish here. Being divisive to this level is already enough reason to leave him out.