They never changed. I'm perfectly fine with this. Even if the Rainboom didn't happen in these timelines, their talents still stayed the same.
My question is, how did they earn their marks in these AUs? In the Crystal War Timeline, I think Fluttershy would've earned her mark first, since she was stranded on the ground with critters. As for AJ, her aunt and uncle might've realized she wasn't suited for city life and urged her to return home.
What do you guys think?

I agree for Fluttershy and Applejack, and I feel that after Rainbow Dash failed to win the race, she would want to get better, and so would push herself even harder than ever before. For Rarity ,she would likely have discovered her aptitude for style eventually. Pinkie Pie and Twilight I feel would both have different Cutie Marks.

Did we ever see Rainbow's mark in any of the AUs? I thought she was always wearing armor, or a suit, or something.

I gotta wonder if it would be the same.

We don't see Dash's cutie mark in either timeline, but it is safe to assume that it is the same.

Pinkie and Shy had their own marks in Chrysalis timeline, and Rarity had her own in Nightmare Moon's one. Applejack considered the farm to be her home, so her mark should be the same as well. And cutie marks seem to state what is your life's purpose, not the other way around. So by that logic they should always be the same.

So it seems that stopping the Rainboom only prevented them from becoming friends, not them discovering the purpose of their life.