Honestly not sure! My instinct is that it will suffer from the problems you mention, but also I've never liked subtitles - I think they give the impression of something lesser. I feel like that might exacerbate the issue since if you're turned off by a 3, you're almost certainly going to be turned off by an X:Y.
It probably doesn't help that the subtitles that come to my mind do the opposite of splitting from a main series, instead denoting some sort of continuance, like Mount & Blade: Warband, and XCOM: Enemy Unknown/Within. The "lesser" feel is much reduced with these because they're both established, well-known franchises.
But the game is still in pre-production so who knows. Could go in any direction as we move along xD If I get flooded with "do I have to play SM1&2 to enjoy this?" questions, yeah, that would probably encourage me to do something differently.