The one thing that I don't like about fan games is that they're typically/always for PC. I live with my dad on the weekends (where my pc is) and my mum during the week (no pc there), so I can't play during the week :(
I love R.O.W.E because of the achievements/goal system and I absolutely adore the UI. <- I'm pretty thats R.O.W.E, haven't played in a little bit
I like Quetzal because of the customizability and also how pokemon walk around in the grass instead of walking through the grass and praying your butt doesn't get bitten by some random pokemon and you gotta fight that dude. It's so hard to go back to normal pokemon emerald without it because of that feature.