The project shift from DSi to 3DS was made solely due to browser capabilities, not exclusivity. Simply put, the 3DS's memory advantages and greater processing power were deemed to be worth it, despite the DSi community being much larger than the 3DS community.
Aspects of TMJ that the DSi browser can support will be on that platform. As the game engine nears completion, I will gauge how well various parts of the game will fit. It's possible that MMO elements may work with less characters on the screen at once. Only time will tell.