Cleaner on paper, but I think the paintings are very good too. They're different, and the two have good and bad things about them. You're a great artist in general, so you don't need to worry about it.
In a way, ponies do look better, or at least more natural when in a 2d setting, when you paint and add colors, in your style at least, depth and form becomes far more of an issue, something that does not lend itself to that feeling that many are used to from seeing the show.
So while pencil with basic shading allows for far better emphasis on line and shape, the color lets you expand into feelings of mood, and emotion in ways that pencil don't.
The old phrase "to each their own" suits this situation rather well, each one has it's ups and downs, and I would say continue to practice in both, but focus more on whatever you prefer, that said, I personally think that with more practice, you can go farther when using color than just graphite.