While I haven’t read all the IDW comics (and probably never will), I did enjoy reading some of them, like the one with Chrysalis (who got her best treatment in her unfortunate situation in the franchise), Nightmare Rarity, the one where Big Macintosh meets other ponies, the clown admired by Pinkie Pie, the one where Twilight looks after a writer, etc. There was variety.
In the Equestria Girls products, there was barely any diversity the IDW comics have. The stories were mostly focused on either stuff for teens or pop songs. In the first movie there was a popularity contest, in Rainbow Rocks there was a music tournament (when it should have been on how Sunset is dealing with rejection because of her actions in the previous film) and Friendship Games was about another tournament. The only exception to me was Legend in Everfree because it was focused on nature, which seems appropiate for kids and teens.
Because of that, I think you can find diverse concepts in the IDW comics and Friendship is Magic than Equestria Girls. Whether someone was better than the other, that’s another discussion. But I wouldn’t say Equestria Girls is underrated, especially when:
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When Rainbow Rocks came out, every single fan loved it from beginning to end.
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It got so much stuff. Again, four movies, many shorts, many music clips, a TV show… So the word “underrated” doesn’t apply in this particular case.
That said, my favourite EG films were the first one and the fourth one, but it’s really hard to go back to watch these films again.