No way, Mother is very known and miles away from being obscure. I think obscure games are underrated games that come from out of the blue or involve a character(s) from a TV show or movie. Nobody's probably never even heard of these, except for maybe like one, but a few obscure games would be: Ghosthunter, Ardy Lightfoot, PK Out of the Shadows, Tak and the Power of Juju, Mario Teaches Typing, Finding Nemo (the game), etc.
Okay, THQ makes some of the weirdest ****. It really surprises me when people call Super Mario RPG "obscure", especially since some/most of those six I mentioned up above haven't even been heard of by many, and I completely forgot they even existed.
About every Nintendo game that was developed by them and/or their subsidiaries is not obscure, considering that Nintendo is one of the most known gaming companies to this day. The Smash series also introduced people into Nintendo's other gaming franchises, including third-party franchises, and in this case it was able to get the Mother series to be recognized.
Think about it this way: If the Mother series was somehow obscure, I don't think EarthBound would be on the SNES Classic. I believe any Nintendo series that's recognized by Nintendo in any shape or form is not obscure.