If Pokemon was also on non-Ninty systems, it'd sell more. The series would only become more profitable, and Game Freak along with it. The fact that it's an exclusive is a negative for everyone but Nintendo by that very reasoning: Game Freak has less sales, and people who are either not willing or are too poor to buy a 3DS just for Pokemon don't get to play the game they want to. If it were not to be exclusive, you're right: it'd be a negative effect. For Nintendo solely. That's proof for my point, exclusivity does nothing but benefit whatever company that procures a title/series. No one else. No middle man, not the gamers, not the developers, only the suits benefit.
So, if Ninty's handheld(s) would decline in popularity and thus sales 'n profitability, what does that tell ya? Title exclusivity is a tool to sell consoles, nothing more. If game exclusivity was thrown out the window, Ninty would no longer be so clearly on top of popularity charts. Only a very small amount of stupid people would ever buy an Xbone. It'd be a battle of who's making the better console, not who owns the best developer studios.
Obviously I can't say for sure whether or not the removal of exclusivity would be nothing but beneficial for gamers and developers alike, but the practice has it's downfalls. T'is my point, that exclusivity is a negative trait of gaming that perhaps should be outright destroyed, or at least done better. For example, exclusive titles would only have their "exclusive" status for a year or two, and be released later for other systems after a set period of time. So long as other systems would get an otherwise exclusive game eventually, assuming developers do want to port the title(s) in question, I wouldn't complain 'bout this issue at all.