This are the female characters of Sonic and MLP that I think they have more in common:

Rainbow Dash & Wave the Swallow: This one might be a little weird, but I have resons to put them together: Both say that the are the better in what they do (RB flying and Wave in mechanic), both aren’t good losers, they are very competitive and doesn’t like the ones that are better in their specialties.

Cream the Rabbit & Fluttershy: They have a lot of things in common: Both have a pet that is really cute (Cheese and Angel), they do not like violence, they are polite, kinda shy, sweet, gentle and they take care of the animals (maybe Cream not all the time, but she always takes care of Cheese and Chocola).

Twilight & Sally Acorn: I know, yo might ask why I did not put Blaze instead of her, well, I do not think Blaze and Twilight are similiar. I think Sally it is more than Blaze, why?: Both are princesses (Blaze too), are intelligent, they have always someone to help them (Spike and NICOLE), I can say that the are the leaders of their teams, they fight for their friends/family, assume their responsabilities and they are always searching information for being sure of everything.

Bunnie Rabbot & Applejack: Only looking at their physical characteristics you see that they are similar, but also in the personality: Both have hats, southern accents, they are honest and generous, really strong, loyal to their friends, they always are there from them and also have a vegetal as favorite food (apples and carrots).

Rarity and Rouge the Bat: As Bunnie and Applejack they have similar physical characteristics and personalities: They are white, have A LOT of passion to the gems, they have blue eyeshadows, are glamorous, they can find easly gems and always are after them.

Amy Rose and Pinkie Pie: As the last two, they are common in both, physically and intellectually: They are pink, they like ice cream, they are obsessed with something or someone (Sonic and Fun) and they do not like the ones that are against with the most thing that they like: Example: Amy hates when someone says something bad about Sonic and Pinkie Pie when someone says that someting that is fun to her it is not (or that is what I think).

This are only MY OPINIOS, the ways I think the female Sonic characters and MLP FIM are alike.
Hope ya like it!

Wave, Amy, Cream, Rouge, Sally and Bunnie belong to SEGA.
Twilight, Fluttershy, Applejack, Rarity, Pinkie Pie and Rainbow Dash belong to Hasbro.