If anything, this should raise others' hopes up about whether or not we'll see the remakes.
Pokemon available/not shouldn't be really seen as a deal breaker, haha.
ALL Pokemon were available in the Advanced Generation of games(Gen III), even if not by normal means, so we can probably tell that HGSS were made for other reasons besides availability. With that in mind, I see that as something to look pass a little.
Although...the absence of the Weather Trio and the other legends not included in BW2, that actually might mean something.