I love them both equally. Each have their own unique charms. The world and clothing of Equestria is better in FiM. I enjoy watching the pony mannerisms in FiM since writing is do unique. Fluttershy is my favorite pony, it feels like she's just there in EQ.
But I'm big on the villain redeeming themself type of character so I love watching Sunset Shimmer grow in Rainbow Rocks. Watching pony Twilight try to figure out "This Strange New World" was my favorite part of Equestria Girls.