I feel that Super Mario Run is part of the main series as, not only does it bear the "Super Mario" name and is a platformer like the original Super Mario Bros., it also is being worked on by the developers by the original Mario games. It might not have everything in common with the traditional game, but I think that the fact that Nintendo treated Super Mario Run as a big event (remember 2016's iPhone reveal, where Miyamoto shows up live?) meant that they treated it as a big game.
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