Well, for one, I don't think that they will have any problems selling the 3DS. It's pretty much a given that it's going to sell well. However, it's going to take a little while before kids will be able to get it, since the high price point will make it more of a system for high schoolers on up. And since one of the major audiences for Pokemon is grade-school children, I can see one of two options happening:
1) Pokemon "gray" is the same type of game as B/W, that is, a DS game with DSi enhancements.
2) Two versions are sold: a DS version and a 3DS version.
Also, what do you think the chances are of them adding in new pokemon in the third game? Like, expanding the pokedex with 20 more creatures. They had some really good ideas for pokemon in Gen V, and I'd like to see some of them expanded upon. I know it's probably unlikely, but there's no doubt that it'd cause the third game to sell more.
As far as the mascot discussion goes, please remember that the "third game" in the first generation was BLUE, not Yellow. We just never really got Red/Green. Yellow was more of a side thought. And I agree with whoever said that Celebi should have been the mascot, not Suicune. But I just don't see Genosect happening. I think Kyurem is really kind of a given.