I will like to start this tread to help summaries the many good reason as to why Twilights transformation into an alicorn was a bad thing.
I will like to make a list and progressively add and expand it as people comes with good logical reasons. Counter arguments are of course also welcome. I want this to turn into a logical and factual presentation of her change that reflects all the lore and wisdom of the community.
1) The balance of the main six are ruined by the change
2) Twilight didn’t deserve to be a princess at least not anymore then any other of her friends.
I can’t think of anything more right now, but as I said, come with ideas and I will add it. I also saw something really intelligent that Dragon Theology wrote on the Magical Mystery Cure page http://mlp.wikia.com/wiki/Magical_Mystery_Cure#comm-310656
The problem with the destiny thing is that it was presented in a Deus Ex Machina kind of way as a lame excuse to convince the viewers that the alicorn thing was in fact planned from the beginning and quickly rush the idea of princesshood without any buildup. The structure of the episode itself had a message that was almost contradicted.
And if you are gonna make her a princess, fine, but why mask it as destiny and do it so early. This leadway to "next level" to princess only took like 11 episodes for her and she didn't even do much in those other then beat Trixie and help organize an event. Clap, clap..well bravo Twilight.
Now I'm not here to debate whether she earned it or not (she actually does in a way; she just needed another season or 2 to develop a real leadway), what I'm trying to say is that this whole "destiny" thing seems like the writers way of implementing an alicorn onto a main character which (as you can tell) practically nobody wanted. And while alot are stupid reasons, some have really valid reasons for not wanting the alicorn thing. This might be explained better in season 4, but as it stands, this was a weak ending and explanation to an otherwise very good episode.
Which ads a valuable third point
3) The transformation was rushed and contradicted the message of the rest of the episode.