From the very beginning, the Pokémon games have been about socialization, and were designed to promote that. Not only were there different monsters in different versions, some of them only ever evolved into their strongest forms when traded. Developer Game Freak and creator Satoshi Tajiri wanted to encourage gamers to meet with their friends, trade and battle. You always could do it on your own, buying two Game Boys and two copies of the game - though that's going against the whole spirit of the thing.
The diehard Poké-fanatics would spend the money on all the games and events in order to hopefully complete their Pokédex, but they didn't have to. If one gamer collected Mew from an event, the gamer could (in theory) trade it to someone else, who could trade it to someone else - and so on. Like baseball cards or stamp collecting, including these ultra-rares should have encouraged gamers to trade, not prohibited it.
It's more than that, though. Having these all-but-unobtainable Pokémon makes it all the more rewarding when you finally catch one against all odds. I think back to the summer I worked at the Pokémon Center store in New York City (now Nintendo World), where we had a special machine that would give out one of the rare legendaries - at the time, Jirachi or Deoxys. I remember watching kids from all over the country who rushed up to the machine with their parents in tow and hooked up their GBA, and I remember how overjoyed they looked to get their hands on this digital treat that they'd maybe heard about in school or online.
I cheated to get my Jirachi. I cheated to get my Deoxys. My friend let me borrow a hackable GBA cartridge that I used to whip up Pokémon from the aether and transfer them into my DS game, tricking it into thinking they were real. When all was said and done, I wore no such overjoyed expression. I'd manipulated numbers, that was all - and numbers were all I had to show for it.
There was no effort in what I'd done, only time spent. A machine or a clever computer program could have done the same thing. There was none of the thrill of a desperate battle as the legendary Pokémon resisted all of your attempts to capture it - and none of the elation when that Pokéball finally clicked shut. With no challenge in the catching, there was no reward. In my quest to be a Pokémon master, I'd ended up missing the point entirely, and done something I would have never considered doing in Super Mario or Banjo-Kazooie. I wanted to collect things - now, I merely had them.
Once upon a time, I caught 'em all.
I really wish I hadn't.
I heard John Funk likes Mudkips.