Oh, oh, what if he walks up to her, and he's like "Hey, Twilight!" and she's like
Human Twi: Do I know you?
Flash: Um. Yeah? I like your new glasses, by the way.
Human Twi: These aren't exactly new.
Human Twi: I think you have me confused with someone else. *Walks away*
They're gonna think she's pony Twilight! Except Pinkie, who has apparently seen her before, considering what she said in the first movie.
But yeah, as soon as I realized the doll was human Twilight, I was like "Ew, that's awkward and weird."
I really do think that if they naturally develop an interest in each other (instead of going "*Bumps into* Oh teehee you're cute let's date"), it'd be better for Flash to be with human Twilight. Pony Twilight won't be there most of the time, and he misses her. He can have an actual relationship with human Twilight.