MrEnter made pretty good points on this when he reviewed Magical Mystery Cure and I'm going to share my opinion on the alicorn drama and why alicorn OCs aren't that bad.
By it's literal definition, a Mary Sue is a character without flaws. In other words, poor writing. If a character screws up just as often as they did when they were a pegasus/unicorn through ascention there's really no issue. Are Alicorn OCs overpowered? Not really. All they do most of the time is either have both magic and a pair of wings. For one, most unicorns (at least the ones we've seen) can create wings for themselves through magic, so it's really not an issue. Two, Twilight Sparkle wasn't Miss Perfect Role Model after becoming a princess. She still lacked Celestia's experience and wasn't an absolute sage when it comes to magic either, not to mention she couldn't fly by herself in the episodes following Magical Mystery Cure.
While I wouldn't recommend alicorn OCs as they are incredibly difficult to write well, I can't say they're all bad either. Truth be told, the only reason I made my OC an alicorn was because he wasn't from Equestria and got his powers from an ancient alien race similar to Superman. But what did Superman have that Mary Sues didn't have? A personality. And that's honestly what's important. If there's no contrivence for the character becoming an alicorn (i.e. they don't just become one for no reason) and they are still likeable and relateable, I really see no issue with it. Sadly this isn't going to be a long rant as Grovyle said a few of the things I'd like to say and I'm simply stating my opinion.
If a character is well rounded, they have flaws, they can be whatever the heck they want. Even though being an alicorn means you are on the same level as Celestia, I don't see that to be true. Celestia is the ruler of the entire land and as long as you aren't taking her place, there's no real issue here.