The Eeveelution theory is the only one that makes actual sense! Look at the facts:
1. The Brass Tower burned down, like what, a 150 years prior to G/S/C? Maybe Vaporeon, Jolteon, and Flareon weren't identified back then, hence the "unamed" Pokemon.
2. Before you can reach the Tin Tower to capture Ho-Oh in Crystal, which requires the three Legendary Beasts to be captured, you must battle three monks, each of whom has an Eeveelution representing fire, Water, and Electricity. Coincidence? I think not!
3. The Kimono Girls in Ecruteak, which is where the Brass Tower burned, each have a single Pokemon, which just so happen to be, the Eeveelutions. Three of them, each have a Vaporeon, a Jolteon, or a Flareon. Another coincedence? No!
4. Bill's presence in Ecruteak when you awaken the Beasts is a little fishy. I mean, Bill is an Eevee enthusiast and after he fixes the Time Machine, he gives you an Eevee in Goldenrod. Eevee evolves into all three, Vaporeon, Jolteon, and Flareon, which the Beasts were reborned from.
5. The lack of evolution stones! In R/B/Y/G, you could buyan infinite amount of Fire, Water, and Lightning Stones. But, in G/S/C, you can only get a handful, and that's being generous since you have to get them from Trainers you've defeated, or from Bill's grandfather in Kanto during the postgame. Now, why wouldn't there be evolution stones in Johto? Could it be to prevent us all from getting an Arcanine, or a Raichu? No. But, to further enforce the theory that Vaporeon, Jolteon, and Flareon are the forms of the Legendary Beasts prior to reincarnation. How? Because, the three "nameless" Pokemon that became Suicune, Raikou, and Entei, are supposed to unique. So, you must either wait til the postgame, or go through mindnumbing hours of hoping for a call from a Trainer to get a stone, which more often then not, is a useless Leaf Stone.
Okay, these 5-points may seem more like things I came up with, but they do make some sense!
