Yes. But as I mentioned before, there are other factors at stake. The most important thing here is to choose a character that fits the series and is appealing to the Smash audience. And since said audience is comprised of Nintendo fans, then a strong presence on said platforms is quite relevant. It doesn't have to be the most popular character, just popular enough.
If it were purely a popularity contest, then Mega Man wouldn't be in. Even just looking at Capcom, Leon S. Kennedy is arguably more popular, and probably around as popular as Snake. But Mega Man was one of the most requested 3rd party characters from Nintendo fans, and he fits the nature of the game more. The same applies to Simon Belmont and Bomberman, in my opinion.
Of course, these are far from being the only alternatives... Not to mention how you don't even have to put another 3rd party character in there. There's plenty of Nintendo characters that could benefit from being on Smash, like Marth, Roy, Lucas and Pit were, while being appealing on its own.
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.