First of all, Next Level Games are developing this title with Tanabe. The reason why its on 3DS, and not Wii U, is because they're more familiar with the console (Luigi's Mansion Dark Moon). So there wouldn't have been a way to change it on Wii U unless NLG was able to adapt quickly to the different specs of the console.
Second, I don't know if a F2P model would've made any difference. In fact, because of the historic perception of gamers on F2P, I think the reception would've been worse than it already is. Probably the best thing they could've done was change the name so it wouldn't be given as much backlash because Prime is highly regarded by the fans and critics. You can still make it and call it a Metroid game without putting in the name Prime in it.
But in the end, it is what it is. A game that received backlash before it could even be played by the public outside of E3.







