I'm sorry? I apologize if I sounded mean in any way. I was simply arguing a point, that's all. And if you want to stick to Gold and Silver that's perfectly fine. That's where some of the more infamous unusable Pokemon come from, and it's a very nice region anyway.
Anyway your post is huge so I'm not gonna post all of it, just respond to it bit by bit. Concerning rare sucky Pokemon like Quilfish, those actually would be rare. They're based off of species like pufferfish that are hard to find in real life, thus they're hard to find in game as well. You only find pufferfish in specific areas, and as a result they can be hard to find. There's also semi-rare rodents that live near water like muskrats, which Marill shares a habitat with (Water's Edge), and Marill is by no means a terrible Pokemon. In general the rareness of a Pokemon tends to match well with the animal it's based off of. If it's something common like butterflies, moths, fish, rodents and pigeons then their Pokemon equivalent will be every bit as common. The exception to this rule is Gyarados, which for some reason is obtainable everywhere you can fish.
As for their suckiness, not taking into account the weakness of the species they're based off of, you sadly can't have every Pokemon be at the same relative power level. That's a basic problem concerning video games; if you make every character powerful, you run the risk of most of them becoming the same. Maplestory's character roster is a good example of this: it originally started with just 4 basic classes with 3 class branches per class. Each character had different powers, and had different strengths and weaknesses, much like Pokemon. Some were more useful than others, but they were different from each other. Then came new classes. Loads of new classes. Some of them brought new mechanics to the table, while others were just reskinned versions of older classes. The older classes got left behind because the newer ones were more powerful, and this power creep continued up until there was over 30 different classes. Nexon, the developer and publisher, tried to fix this by radically changing the older classes and giving them flashier moves and removing stat mechanics until there was only one main stat for each class. This "fixed" the older classes, but they lost their identity. All of them ended up having the same kinds of skills and same kind of class mechanics and were pretty much the same kinds of characters over and over again.
Without a gimmick making each Pokemon special you'd run the risk of making them all very similar, and it kills the individual aspect Pokemon has. Each Pokemon is meant to be different, even Pokemon that are expies of each other like Raticate and Linoone. I'm not saying they shouldn't be strengthened; it sucks that some of these Pokemon are as useless as they are. But what happened if you made them all strong? Would they all have access to the same moves, and have the same BSTs? Sure it would be great that you'd finally be able to use them, but just what kind of cost would that bring? You'd have to tread very carefully.
With that said though, I was referring to the Unknown Dungeon in R/B/Y. In there you could find wild Raichu, a Pokemon only available through a stone based evolution. That isn't the only place you can find Pokemon that normally evolve through special means, but it's there. Concerning the Gym Leaders, it should be noted that the teams we battle them with are not their main teams. They have a special team designed to challenge opponents at the proper level without being impossible to defeat; thus they may have a team of much stronger Pokemon they use to go long distances with. Whitney in particular having a Clefairy isn't impossible; Mt. Moon isn't very far away, and the rail connecting Goldenrod and Saffron has been there for at least a couple of years, so she simply could have went over there and caught one. Even if she didn't she could have traded for it, and the other girls in the gym also have them so there's that too. It's a similar deal with Falkner; he recently got the team he uses from his dad, who gave the gym to him. His dad could have captured the Pidgeotto and gave it to him. Even normal trainers having stone based evolutions isn't unjustified, as just because you couldn't get the stones doesn't mean they couldn't.
Going onward, I don't think changing the availability of evolutions (other than the trade-based ones for obvious reasons) are that good of an idea. Especially happiness based ones; you get an Eevee from Bill pretty early in the game, and if happiness was limited to after the Elite Four you wouldn't be able to get Espeon or Umbreon. (Also on a minor note, the in game trades aren't that bad. I beat the Elite Four with Rocky the Onix in my team. The other ones suck though; they should have a Voltorb for a Krabby and a Rapidash for a Gloom. You can readily find Bellsprout in the wild, and you can't find the other two so easily.)
With all of that said though, you're right; we do have differing opinions on this, and that's fine. It should be noted though that even as useless as some of these Pokemon are, you can still beat the game with them. Karen described it most accurately; the strength of the Pokemon doesn't matter. Truly skilled trainers win with their favorites, no matter how weak they may be. You can beat the game with a team of everything but Unown if you're skilled enough.
Anyway your post is huge so I'm not gonna post all of it, just respond to it bit by bit. Concerning rare sucky Pokemon like Quilfish, those actually would be rare. They're based off of species like pufferfish that are hard to find in real life, thus they're hard to find in game as well. You only find pufferfish in specific areas, and as a result they can be hard to find. There's also semi-rare rodents that live near water like muskrats, which Marill shares a habitat with (Water's Edge), and Marill is by no means a terrible Pokemon. In general the rareness of a Pokemon tends to match well with the animal it's based off of. If it's something common like butterflies, moths, fish, rodents and pigeons then their Pokemon equivalent will be every bit as common. The exception to this rule is Gyarados, which for some reason is obtainable everywhere you can fish.
As for their suckiness, not taking into account the weakness of the species they're based off of, you sadly can't have every Pokemon be at the same relative power level. That's a basic problem concerning video games; if you make every character powerful, you run the risk of most of them becoming the same. Maplestory's character roster is a good example of this: it originally started with just 4 basic classes with 3 class branches per class. Each character had different powers, and had different strengths and weaknesses, much like Pokemon. Some were more useful than others, but they were different from each other. Then came new classes. Loads of new classes. Some of them brought new mechanics to the table, while others were just reskinned versions of older classes. The older classes got left behind because the newer ones were more powerful, and this power creep continued up until there was over 30 different classes. Nexon, the developer and publisher, tried to fix this by radically changing the older classes and giving them flashier moves and removing stat mechanics until there was only one main stat for each class. This "fixed" the older classes, but they lost their identity. All of them ended up having the same kinds of skills and same kind of class mechanics and were pretty much the same kinds of characters over and over again.
Without a gimmick making each Pokemon special you'd run the risk of making them all very similar, and it kills the individual aspect Pokemon has. Each Pokemon is meant to be different, even Pokemon that are expies of each other like Raticate and Linoone. I'm not saying they shouldn't be strengthened; it sucks that some of these Pokemon are as useless as they are. But what happened if you made them all strong? Would they all have access to the same moves, and have the same BSTs? Sure it would be great that you'd finally be able to use them, but just what kind of cost would that bring? You'd have to tread very carefully.
With that said though, I was referring to the Unknown Dungeon in R/B/Y. In there you could find wild Raichu, a Pokemon only available through a stone based evolution. That isn't the only place you can find Pokemon that normally evolve through special means, but it's there. Concerning the Gym Leaders, it should be noted that the teams we battle them with are not their main teams. They have a special team designed to challenge opponents at the proper level without being impossible to defeat; thus they may have a team of much stronger Pokemon they use to go long distances with. Whitney in particular having a Clefairy isn't impossible; Mt. Moon isn't very far away, and the rail connecting Goldenrod and Saffron has been there for at least a couple of years, so she simply could have went over there and caught one. Even if she didn't she could have traded for it, and the other girls in the gym also have them so there's that too. It's a similar deal with Falkner; he recently got the team he uses from his dad, who gave the gym to him. His dad could have captured the Pidgeotto and gave it to him. Even normal trainers having stone based evolutions isn't unjustified, as just because you couldn't get the stones doesn't mean they couldn't.
Going onward, I don't think changing the availability of evolutions (other than the trade-based ones for obvious reasons) are that good of an idea. Especially happiness based ones; you get an Eevee from Bill pretty early in the game, and if happiness was limited to after the Elite Four you wouldn't be able to get Espeon or Umbreon. (Also on a minor note, the in game trades aren't that bad. I beat the Elite Four with Rocky the Onix in my team. The other ones suck though; they should have a Voltorb for a Krabby and a Rapidash for a Gloom. You can readily find Bellsprout in the wild, and you can't find the other two so easily.)
With all of that said though, you're right; we do have differing opinions on this, and that's fine. It should be noted though that even as useless as some of these Pokemon are, you can still beat the game with them. Karen described it most accurately; the strength of the Pokemon doesn't matter. Truly skilled trainers win with their favorites, no matter how weak they may be. You can beat the game with a team of everything but Unown if you're skilled enough.