PS - Uh, when I talk about ponies I tend to... reassure people it's just my opinion and I could be wrong more often than other fandoms. If you hadn't noticed. XD

That was the pun, but definitely not. XD

I don't know about G1 pony popularity, but of the Mane Six she SEEMS to be the least popular - ponies like Rarity and Rainbow Dash will often rank low but there's a lot of passion around them (dislike and like), where as AJ just kind of... welp. In my experience, and again this is from my limited view (I try to avoid paying to much attention to the fanbase, we're very vocal and opinionated which while often at levels of maximum awesome... like any other fanbase maximum awesome is always balanced by an equal level of stupid), it's less that she's disliked and more that people aren't... sure what kind of opinion to form. She's generally regarded as the least developed of the Mane Six.

The explanation is probably she hasn't gotten as many focal episodes. Season 3 gave her a great one, but let me do the run down of her focal episodes from my point of view (others may disagree):

An episode where I feel she 'cheats' to win a John Henry type competition with a happy ending and is a complete smart-ass/troll in the ending. One of these days I might do a rewrite of this just so I can have a version I like more (seriously there is only one episode I dislike more than the Super Speedy Cider Squeezy one. XD)

An episode that was actually pretty decent development wise, but got buried due to probably the biggest fandom drama shitstorm I've EVER seen regarding a popular background pony/fanbase shoutout that was on air for like fifteen seconds. That's right, a (arguably understandable although I try to avoid discussion about it because it's still a pretty heated issue - it probably won't burn you any more but it's a sore spot) fifteen or so second bit became more important than a the ~22 minutes of the rest of the episode.

And finally an episode where we got to see awesome, a great song, and one of the best episodes of Season 3 in my overall opinion just because AJ FOCUS AND NO DRAMA YESPLZ.

Of the Mane Six, my least favorite is probably Rainbow Dash - it's not that I don't like her, she's just my least favorite. Fluttershy will occasionally tie with her based on the time of day and most recent episode I've seen, mind you. XD I feel those two ponies are the most commonly flanderized within the show itself (Rainbow Dash is hard to write and it reflects. I would like to mention my least favorite episode was a rather (in my opinion) OOC mess focusing on her. I've watched that episode writer's other episodes though, and it seems she was just having an off day though.)

And again, I don't really dislike anypony (or other character), but I definitely have some that rank lower than others. XD

PS - I could talk to you for HOURS about ponies, so lemme ever know if you're game. XD