I love Pokemon. The games, the show, the toys. All of it. I'm insane for it.
And so here they are.
The best Pokemon game to date was Crystal. You got 2 different worlds, you could collect 16 gym badges, and you could collect all the new pokemon as well as all the classics. There was a good storyline, and best of all, battle animations. Well, not so much battle animations as pokemon animations. Every pokemon had an animation that made it look cool. The only way it could have been improved is if pokemon acquisition was more like Yellow, where you get a special favourite pokemon to start with and then acquire the 3 starters from Gold & Silver throughout the game.
So, when they moved it all to GBA, why didn't they keep the animations? There are so many improvements made in Ruby/Sapphire that I hate to criticize it, but those animations were great, and the opportunity to collect 16 gym badges made the game more fun. I love the contests, and the icons, and pokemon storage has finally become a process that makes sense and is not a pain in the ass. Ability to grow berries is great, too. But my main criticism of Ruby/Sapphire is that it doesn't have all of the original 251 pokemon! I don't understand the logic behind what they kept, either. It almost feels like they didn't want to keep *any* of the originals, but they felt obligated to because of the tv show.
Let me just mention, as far as the Legendary Pokemon of Ruby/Sapphire, you have to look up braille letters. Then you have to decipher loads of stuff in braille, only about 1/4 of which is actually useful in unlocking the legendary robot pokemon. It was a pain in the ass. They're way easier to catch than those flighty legendary doggies from Gold/Silver/Crystal, though. I think the best legendary pokemon were the birds, from series 1. Rayquaza is about the coolest Really Dangerous Only-One pokemon ever, I think. Way better than MewTwo, in my opinion, but other people swear by MewTwo so what do I know. I know that my Alakazam was better than my MewTwo.
One thing I really miss from Yellow is the pikachu following you around. It was really cute. I wish there was another game since that allowed a pokemon to follow you around. I also liked how people would be there solely to give you a pokemon.
Here's what I absolutely love about Ruby and Sapphire: the pokemon storage system, pokemon contests, the new pokemon summary page, the description of attacks and items, pokemon natures, the levelling-up stat info, growing berries, the tv and the interviewers, Record Corner (oh if you haven't tried it, you must. it's too much fun.), Secret Base, all the new pokemon.
I wish it had pokemon animations like Crystal, a pokemon to follow you around like Yellow, and day and night differences like in Gold/Silver/Crystal. I do not feel as connected to my characters in the recent generation as much as I did in the 2nd generation, and I think it's because there is no night and day. The supporting cast seems a bit distant, too. I never really felt like my character and the other characters had a good connection like they did in generation 2. I think it's because they tried to put too many characters in a shorter plotline. There's your rival, and Wally, and Steven, and various other people, and there just doesn't seem to be enough interaction between them and my character to really create any bonds.
In Generation 2, Lance showed up a couple of times, and had discussions with you, so you really felt that you were his friend when you met him again at Pokemon League. But Steven is like, nowhere. You don't get to have enough interaction with him. Prof. Birch and the rival, too. (My rival was Brendan). I wish they'd let me pick the name for my rival. I picked my character name based on a dichotomy and I was hoping to use the rival as the other part.
So, in summary, Ruby and Sapphire are great, but with these changes the next generation would be supreme:
1.) Include all 350+ pokemon!
2.) Bring back Pokemon animations
3.) Let you choose a pokemon to follow you around
4.) Night & day visual differences
5.) More interaction with supporting cast
I think that covers it.