I don't think they'd bother playing that vague recognition angle at all if it had such a mundane explanation. The story purpose of going there seems to be a tease to a larger mystery than just the obvious extradimensional counterpart angle.
Or, he is an extradimensional counterpart, and that's just the first layer of the larger mystery. It's a short season, after all, so it makes sense that we'd start getting
pieces of the answer right away. It doesn't make sense to mistake the first piece for the entire puzzle.
I'm not sayng it's certain, of course, but it's less of a stretch than Snowflake/Butterfly/whoever's crazy talk about reincarnation being factual, or Sarge being a year old.
If this was just a simple parallel universe doppelganger, they'd probably be playing it up as EVIL COULSON Mwhahhahahahahaha, and not the big mystery they're going with.
Again, why assume it's simple? Why assume that
what he is constitutes 100% of the story? There's a ton of who and how and why still to be revealed. Not to mention getting to know him as a
character and exploring his relationships with the other characters, which is what fiction is actually about. The fact that he's from an alternate reality isn't the end of the mystery, it's just the first clue.
I agree with your first point, but as for the second, yes AoS is an ensemble, but Coulson has still always been the main character on the show, with May and Daisy/Skye a level below him. The same way the Star Treks were ensembles, with the captains as the main characters and the others a level or so below them.
Ensembles change composition all the time. Sometimes the members of an ensemble are shuffled in importance. In
Legends of Tomorrow, season 1 centered on Rip Hunter and his quest. In season 2, he was reduced to a supporting character. And there have been a number of shows where initially supporting characters have overshadowed the nominal leads, like
Happy Days or
Family Matters.
Besides, where's the value in saying that nothing should ever be done differently than it's been done in the past, whether in this show or others?