In my opinion, the Ruby and Sapphire (including Emerald) games (not necessarily including FireRed and LeafGreen) are by far the worst set of Pokemon games. However, I might just be overly nitpicky. Who knows?

I will, of course, justify this, but let me mention something: there were DEFINITELY improvements in this generation to the battling system, separate from the games. I wholely like the addition of Natures and Abilities. However, they screwed up breeding and Stat EXP, two changes I don't like. A lot of my complaints are directed at the games though.

Now: Why Ruby and Sapphire suck.

The biggest reason that Ruby and Sapphire (henceforth RuSa) sucks is because of the modification to the Stat EXP system. In earlier generations of Pokemon games, each stat had a certain amount of EXP, and you gained "Stat EXP" or "Effort Points" by fighting other Pokemon. This feature IS present in all generations of the game, and it is what distinguishes a trained Pokemon from an untrained (e.g. newly caught; collecting dust in your Box; whatever) Pokemon. Two Pokemon of the same species with the same IVs (like a Pokemon's genes. Each stat has an IV that affects the stat you see on the Pokemon's Status screen) could have different stats if they differed in the Stat EXP for each stat. (Count of the phoneme "Stat" in sentence: 6) Each stat's EXP was independent of the others, and, eventually, through much training, you could fill up each stat's EXP value and have one pimped out Pokemon with relatively maxed out stats (IVs also make a difference). This is widely regarded as an excellent move, much unlike the creation of the universe (-10 points for style, God! C'mon, quantum mechanics? Why probabilities?)

However, in RuSa, each Stat's maximum EXP/Effort value is set to 255. This isn't so bad, as a maxed out stat in RuSa will give the same bonus as a maxed out stat in GSC. What sucks about the RuSa system is that an individual Pokemon can only have a maximum 512 TOTAL Effort Points across the board. This means that your starting Pokemon, the one you raised and loved from its reception, will probably have crazy, undesired effort value growth (in otherwords, your Pokemon will suck for competitive battling). This is a Bad Thing. This is merely a gigantic inconvenience for anyone playing for battling purposes. We hate this! Oh, Nintendo, why must thou be so evil?

Another reason that RuSa is the worst set of games is the breeding system. Essentially, the Pokemon's IVs are inherited randomly. Up to three (because of a glitch) separate IVs can be inherited from the parents. All other IVs are determined randomly, which throws another monkey wrench into the proverbial printing press. This is utterly stupid and somewhat self-defeating. With this system, one lacks the ability to breed for the best genes of the offspring, as the IVs are so much more random than in GSC. Combined with the effort value system, this makes breeding/training the best Pokemon of a species a real bitch.

Now, as for things unique RuSa themselves:

One reason they suck is the Contests, which are utterly pointless. Some may disagree with me here. In actuality, the only purpose Contests serve is to get ribbons and stuff, and provide some sort of alternative, wussy form to battling (OMG MY POKEMON IS HOTTER THAN URS!!!!!!!!11111). One can easily ignore the contests. I choose to, personally. It just seems like a bit of a denigration to the series, though.

Another reason that they suck is because of the high abundance of special event Pokemon! Deoxys, Jirachi, the sibling in Latias/Latios, Mew, and the yet to be seen Celebi! Whatever happened to, you know, putting them into the game? I mean, I know Mew and Celebi were "secret" in earlier generations, which was still a bit of an annoyance to those who couldn't get to the conventions. But now, if you want to catch every Pokemon (nobody does anymore), in addition to buying the twin cartridge in the series, and buying BOTH FireRed and LeafGreen, you also have to buy: an e-Reader, another GBA, a link cable, the cards which give you access to the Pokemon, GBA-GameCube link cable, Pokemon Colosseum, another memory card (it takes up a full memory card, Colosseum), and the Pokemon Colosseum pre-order disc ($15, or more if you get it from eBay). Now, I don't know about you, but even to my white, relatively well-off suburban middle-class status, this seems like A Lot Of Money. In previous generations, for the secret Pokemon, you only had to find a ride to whatever convention Nintendo held, which might take up time AND money, but at least not a lot of money. Nowadays, they just give out so much stuff through the Pokemon Center in New York that you probably have to factor in airline costs when you get the price of the cards required.
I am fairly certain that, when you add it all up, you will probably be paying at least 1 USD for each separate species you catch in this generation.

My final (?) reason in support of RuSa's suckage is Nosepass. A weak, ultimately stupid Pokemon. I don't think I need to elaborate much on this. I mean, how much suckier can you get than NOSEPASS? Its suckage emanates from itself, spreading its suck to RuSa itself.

This is why it is my firm, undying belief that RuSa are indeed the worst Pokemon games of the main series ever made by Nintendo. And you can convince me otherwise only when you pry the Pokemon Crystal and FireRed cartridges from my cold, dead hands.

Forgive my rant.

* Yes, people, I am joking. This contention has no logic to it, other than personal bias. So don't actually take it as a reason.