You aren't buying 3 games to play one. You are buying 3 games to play 3 games. It makes it so your character transitions into another region, rather than starting from scratch. In sports games, where you create a character and you try to get that one character to be a star, you can transfer your character from a previous year in to the next iteration of the game, and continue from there. It isn't any different from that. It also allows you to create a new character for the new region (starting over) rather than transferring your character from the old region (continuing). It also makes it so that each region isn't isolated, and the world is actually one big world where you get a game, start from one specific region, and as long as you have the other games, you can freely enter another region. For people who didn't buy the previous game, as I said, you can still start a new game in the new version.
I think in the madden series, you can import a player from the NCAA college football series, at least in the 2010 version of the games anyway. This would be no different from that. If I buy NCAA football 10 and Madden 10, and import my NCAA player into Madden, am I paying for 2 games just to play one game? No.
The biggest problem though is Pokemon does have a level cap. Once you hit Level 100 there's nothing beyond that. You'd have to pretty much lower the levels of everything so by the time you do get to the third region, everything's Level 80+ and at that point it's a "Why bother?" situation. GSC/HGSS did it best by having Johto "end" at Level 50 and Kanto "end" at 80 because it gave you the content to reach that high. For three regions to work would mean having to lower the levels and experience tables of everything which would subtract from the experience of the games.
And you can't really compare Madden of all things to Pokemon. They're in completely different genres with their own gameplays. And now the next problem is that what you want is a more "anime" like experience with you traveling to different regions with your team. But the anime doesn't do that. Ash restarts all of his teams in each region with the exception of the beginning of Johto and even then it was blatant in its message that Charizard versus Chikorita is unfair. It sounds more like you want an "MMO" styled game, which doesn't work for a different reason. MMOs aren't casual. Pokemon is a casual game. You can be competitive, sure. But many people love Pokemon for how relaxing it is to just sit down and play. That's why you can't have a super gigantic Pokemon world in a single narrative. At some point you will hit a wall and stop enjoying it.