1.Caves and water routes
Zubat, Tentacool, geodude, can you just NOT. It's not about how often they appear, it's about how pointless they are to be beaten. Minimal EGP gain, and no fun at all.
Cave and Water routes are absolutely painful. especially the one in R/S/E, where like a quarter of the map is surfing routes. Even if the pokemon were switched up, I do feel like It'd still frustrate me..
2. Too many trainers in one route
"Alright, time to move forward, lets see what we have on the next route" And bam, 10 players almost one near each other. That route in Kanto, right from the town with Safari. Why so many trainers?!
But I guess it's not that bad.
I don't have a problem with these routes once they
promote the equal growth of all my pokemon. If it's a route where "Oh look, another bird tamer. Guess you'll be sitting this one out too, Chicorita. If there's a wide variety of Pokemon that I do have to think about, then I feel I'd prefer that.
The other thing about this is, especially in some hacks, I feel like it just isn't done very well. IMO you need to be a decent bit into the game (at least level 20's) before they introduce a big barrage of trainers that you have to fight. That or the trainers should be that little bit lower levelled. Especially when the routes are super duper long.. Maybe I've been playing the wrong hacks though... :)
3. Not being able to train some Pokemon from the beginning
Someone already mentioned it. Dratini, Eevee etc. In most games they are either unobtainable or hardly obtainable at the point where I'm almost done with the main game.
I do have a solution for that though, in Pokemon Soul SIlver which I am planning to play sometimes this or next year, I will trade over eggs of Pokemon I want to play with, so I could do that from the very beginning :D
I feel like the "unobtainables early in" was tweaked a little in X and Y. Like, you can catch Axew and Eevee (among others) pretty early on in the game :) That said, It was really frustrating. Playing through Black I had to wait till I got Surf to get a Frillish, which bothered me a lot....
I agree with the stuff one has to do at the beginning, for us "veterans" its getting pretty annoying.
One thing ive never liked that much is the Victoy Road. Its this huge cave with so many trainers and you usually need a bunch of HMs to get through. I would love to see GF try something else as their "vitory road" in a future game
They do need to make a tutorial skip option! It's just painful being told how to catch Pokemon when you know how! :)
Victory Road ALWAYS gets me. I'm never any good with it, and it's just the last slow boring bit of the game.
This is an answer I can bunk on, I mean it's not like it's easy forgetting WHAT THE VERY GAME IS BUILT ON, but I guess the people at GameFreak studios and Nintendo must've though every pokemon player is new.
I also wanted something with the story-line to differ or to be able to change, like based on what are the decisions of the players and what paths they would take, so that as the story moves along, players could become the villain, the hero, the savior, or the destroyer. It would make a lot more things interesting and not so repetitive in a sense.
I would absolutely love if they incorporated choice-based gameplay. Even if it was as simple as changing around the trainers you have to fight (eg instead of Rockets have Police), it would be kinda cool :)