Let's see...
1. The fact that the only things you can do post-game (other than training Pokemon) are either rebattling the Elite 4 or doing the Trainer Tower challenge. Both get really repetitive after a while. I'd say Sevii Islands as well, but the plot there doesn't seem that long...
2. The lack of Emerald's 'updates', such as the EV-reducing Berries and the usage of certain abilities (Synchronize, Flame Body, Compoundeyes) out of battle. Being able to have more control over the natures of legendaries along with increasing the chance of finding wild Chansey holding Lucky Egg (in the Safari Zone) would've been a major plus.
3. Some of the visuals (the font was OK, I guess). However, I really prefer the RSE Red (overworld sprite that appears in Emerald when you're battling/trading with a FR/LG player) than the FR/LG Red. But I guess the FR/LG style was supposed to go for a more retro look, I guess.
Also, it's a minor weird thing, but if you play FR/LG for a while and switch back to Emerald, the HP Bars in Emerald seem really skinny/thin for a while until your eyes readjust.
4. And the most annoying thing for me, the 60-Pokemon count requirement for the National Dex, plus the Ruby and Sapphire Key Item quest to trade with RSE.
Since no one around me had FR/LG, I had to do the grueling task of completing the game 3 times from scratch to get all the Starters plus the Legendary Dogs. That includes assembling a team that has to be able to both prevent the Dog from fleeing and find a way to nullify the Roar factor. Because if the Dog happens to Roar you away, the Pokedex shows its location as "AREA UNKNOWN" right after that, making you pretty much screwed. If I'd only known about HG/SS sooner... :( :t243: :t244: :t245: I mean, Pokemon is fun, but all that repetitiveness should not be needed just for 6 Pokemon.
That's pretty much it for me. I'm just glad that "catch x amount ofPokemon" requirement is nowhere to be seen in DPPt or HG/SS. :D