Listed from least annoying, to most annoying.
5. No WaterBlue- Now, I know this one seems a bit stupid, but I heard that they had trademarked the name and nearly wet myself. Maybe it was a lie, a rumor, but I would have kept the box if it had Blastoise on it. And the manual. And maybe even the plastic wrapping. I'm biased I guess, I like the other two, but I ADORE Blastoise. XD
4. Removal of MissingNo- I'm awkward. I feel as if MissingNo, rather than being shunned for being a glitched pokemon, should be salvaged and remade into a real pokemon. This was the perfect opportunity.
3. No go for Johto- Please excuse the stupid rhyme, but it seems that with this being made after G/S/C that we might get Johto. We didn't. Instead, we got the Sevii islands. Now, the Sevii islands aren't too bad, but it's no secondary region.
2. No second challenge- Nope. Nothin'. You can't even challenge the leaders again. This makes the point of my next one.
1. TRADE BLOCK- You have to beat the Elite four, have a certain amount of Pokemon and get both the Ruby and the Sapphire to Celio in order to trade in pokemon not originally in the game. Why is this a bad thing? You'd understand if your favorite pokemon wasn't from Kanto. After you've finished the requirements in order to trade, there's absolutely no story left, which means all that's left for your prized pokemon is senseless grinding. That's it. Grinding. At least Emerald attempted to remedy this with the Battle frontier.