Ok, a lot of you seem to have forgotten the many shortcomings of Gen III, so allow me to remind you.
No day/night cycle or days of the week: They replaced this incredibly awesome concept with the much shittier "changing of the tides" feature which barely did anything. Adding a real clock and calendar into the Pokemon series opened up a myriad of cool and unique things to do, so it was a shame to see it completely gone.
Where's that Pokemon?: This generation bumped the number of Pokemon to 386. Awesome, right? However, there were only about 200 Pokemon you could actually get between Ruby and Sapphire. That means almost half of the Pokemon were missing. You couldn't rock the house with a Venusaur or hell even a Cloyser until FireRed/LeafGreen were released.
Poor type balance: Did you pick Torchic at the beginning of the game? No? Then you're fucked because that's like the only fire type in the game. Ok, there are a few, but your other options are Torkoal, Camerupt, Ninetails, and Magcargo, many of those which show up at the end of the game. There were a shitload of grass and water Pokemon though, taunting my Treecko's relevance. Although I guess it was easy to train him since there were so many water Pokemon to kill. Not to mention the woeful lack of other types like Electric, Dark, Psychic etc.
Boring overworld: Hoenn is largely based off of the island of Kyushu, which would probably be a great place to visit in real life. However, the Pokemon world's version of Kyushu is basically an endless droll of the same looking areas covered in water. Ok, the treehouse city was cool, but everything else was either too small or too watery. We could also explore underwater in this game, I suppose so Nintendo could prove that they could take you to an even more boring place.
Worst rivals ever: Remember how awesome the rivals were in Gen I and II? Blue in Gen I was always a step ahead of you, and your rivalry set up an awesome final battle. In Gen II, your rival was genuinely malicious until he had a change of heart (inspired by an ass kicking). In Gen III you are given TWO rivals. Awesome, right? Too bad your rivals are an opposite gender doppleganger that doesn't even fully evolve his/her starter Pokemon and a sickly kid who tries to take you on with a Delcatty and a Roselia.
Natures: You could argue that natures make each Pokemon unique and you can craft each one to your personal liking. This is true. However, you can't select your Pokemon's nature, which means that it could get a nature that messes up it's growth and, depending on the Pokemon, can render it completely useless or weak. If you want your Pokemon to have the right nature, you have go through the soul crushing process of breeding. This is especially sucky at the beginning of the game, where you have to reset each time your starter Pokemon gets a horrible nature. I hope we can select natures in Gen V.
Lame new Pokemon: Many of them are simply retreads of past Pokemon. Oh look, it's updated Rattata and Pidgey! At least give them some cool types or something. Many of the Pokemon were completely useless and forgettable (did you know there's a Pokemon called Gorebyss? You forgot about him, didn't you?). There were a few good ones (who doesn't love Metagross?) but many of them were uninspired and not worthy using or catching.
And some other nitpicks that I won't mention. That being said, Gen III is still enjoyable. I thought the story was good and it did a good job expanding the mythos of the Pokemon world. From a battling standpoint, there were a lot of interesting moves, double battles were gimmicky but fun, and the weather effects during battle added a whole new element (and also made battles five times longer than they should be). Also, I hate to admit this, but the contests were strangely addicting and gave me something fun to do beyond fighting water Pokemon. It is still without a doubt the weakest generation, despite it's innovations.