The reasons are many. To sum up most of them, it's a fun episode with a well-written plot that is logical and balanced, comical, and tells your staple MLP story about character growth, etc. But I confess that the prevailing reason why the episode has so long remained the unchallenged most favorite is the more bias one.
I'm a sucker for time travel stories.
Why do you think I'm a Whovian, among other things?
It helped that the very idea of MLP telling a time travel story struck me as such an unlikely one that, when it did happen, and was so wonderfully rendered too, I was rather blown away that it had taken place. It had struck me as the one episode where MLP opened a can of worms it normally didn't, and the implications and full ramifications of that were...intriguing. As such, the episode has always had a special interest with me, and still does.
But the one thing I thought the show needed to do, it was come back to it; "It's About Time" opened that can of worms that is time travel, yes, but it was clear it would take a whole new episode to explore where that can of worms could go next.
So in a way it kind of figures that the episode that can actually rival "It's About Time" as the top favorite is the one that does precisely that.