I don’t have too much of a problem with Sunny becoming an Alicorn at the end (Even if it’s rather strangely designed which some have said may mean it’s only a powerup of some kind). As it could be argued Sunny has earned it over years of trying to unite the ponies (It’s just screentime wise, we got to know Twilight over the course of 2 1/2 seasons before she ascended. Plus the implied studenthood under Celestia ever since she was a filly. Of which was unclear of what she was being trained for, up until she ascended)
Though uh… it does sort of entrap the writers of the series in quite a few ways. Alicorn lore is something not even G4 really answered all that well, and I’d understand the frustations about that for FiM originally. The ending of the G5 movie however makes sure that they inherit this issue faster then it would otherwise.
You already have so many questions hurled at the writers team based on just the premise. Now you have whether Sunny’s form is permanent (She didn’t turn back before the end of the movie, plus there’s concept art of
a more permanent looking Alicorn form suggesting that at least at one point, this was going to be permanent) or not added as a question. If it is permanent, why the quite different, glowy design (…Other then the cynical look at it by saying it’s just to match the design of the toy), and will she be acknowledged as a Princess are added as questions that may need immediate answers. And even if it
isn’t permanent, there was never a case of temporary alicornication for the sole exception of when Cozy Glow was an Alicorn in the final two-parter after receiving power from Grogar’s Bell. And the horn and wings looked just as part of her body as the other Alicorns. Could be seen as something of an overreaction to what went down when Twilight ascended “Uh…. the fan base split itself when we ascended Twilight. You sure we want to do that again? What if we met it half way, made it a power-up of some kind?” though that method having some head scratching of it’s own.
Alicorns have generally been a head scratcher even before Twilight ascended what with Cadence’s debut and the many different interpretations of Luna’s personality before she finally appeared in Luna Eclipsed. But Sunny seemingly becoming one certainly brings that issue up to the forefront again. Not to mention how this easily branches into the other questions. We don’t know how long the timeframe is exactly between G4 and G5. But we know Celestia and Luna have lived for more then 1000 years. And it’s not like they looked all that old when they retired. So… what was the fate of all the Alicorns we knew? You have Celestia, Luna, Cadence, Twilight, and young Flurry Heart. Maybe even potentially Luster Dawn if perhaps she eventually went that far as Twilight’s student.
Either way, it’s so many questions. And not many easy answers. It’s just another of those things that would have been easier on everyone (On both fans, and the G5 writers and staff) if G5 had been it’s own world like every other MLP generation that had a show, or at the very least G4 was fictional in G5’s world in a very meta sense.