Yes, there really is too much water.
I will be one of the first people to admit that I don't like Gen III. I think that Ruby/Sapphire set a lot of negative trends of the Pokemon series that fans are still trying to grapple with today. I will fully admit that while the changes made to Ruby/Sapphire were necessary, they were handled very poorly and the overall results leave me very mixed. I'm downright confused as to how many fans call it their favorite Pokemon generation, but I will not harp on them for their own opinions. Instead, let me explain why I think that Gen III is the most flawed generation in the franchise.
Gen III had a steep decline of Pokemon fans and could easily be identified as the end of the late 90's-early 2000's Pokemania. It wasn't because of the quality of the game though. Even though I'm about to bash Gen III like never before, I can't blame it for marking the end of Pokemania. For Gen I and II, you could conceivably play both of those games on one handheld. If you had a Gameboy Color, you had all of the Pokemon games on one system. You didn't need to go out and buy a new system the keep up to date on the world of Pokemon. However, with various hardware updates and the Gameboy Advance becoming more popular, in order for Pokemon to survive, it needed to make a hardware jump. Unfortunately, not everyone had enough money to pay for a Gameboy Advance and a new game, so a loss of fans was to be expected. However, Ruby/Sapphire tried to update the game in new and interesting ways to very divisive results. I feel like now that it's been 12 years since Gen III was released and several months since I've played through its updated remakes Omega Ruby and Alpha Sapphire, I can judge what worked, what didn't, and fundamental changes in the philosophy of Pokemon design.
For example, Ruby/Sapphire was the generation that began the new Team ________ storylines. Every since Gen III, all Pokemon games have made it a significant point to include a side story to the main game where you must defeat and evil Pokemon team before the 8th gym from them conquering the world. It usually involves a legendary Pokemon and a ridiculous plan that would never work in any other game ever. I don't think we need to reiterate how stupid Maxie's plan of removing ALL WATER ON EARTH truly is. The problem with these forced storylines though is simple. The entire point of Pokemon is to beat the Elite 4, become the Champion, and capture Pokemon to your heart's content. You can't do that when the game physically stops you and limits you on where you can go and what you can do until you beat this forced story event. You're meant to be free, not tied down to a plot that no one cares about. Gen III at several points stopped your exploration, forced you to go to a set location, beat enemies that all used the same Pokemon, then allowed you to continue on your quest. It grinds the game to a halt, and being sent of medial tasks is not what I want to do in a Pokemon game.