To answer the main question of the thread, yes, Nintendo should REALLY think about locking this project up!
I feel like they got a bit cocky after the success of the Wii, rested on their laurels, happy to churn out the next instalment of their major sellers on home and hand-held consoles, but running a bit dry on innovation. If they could make it use motion controls, it got the green light, they'll think about the design bit later, and the novelty for the players wore off - a while ago.
What the guys at Playtonic are shooting for (long and short term) would give the Nintendo brand an injection of fresh IP to play with whilst upholding their values of games that are non-offensive, challenging and engaging, but overall just FUN!
Nintendo's announcement that they're branching out to smart devices and a new console
suggests that they've acknowledged they've got some ground to make up and they're being a bit more open-minded. If they can't see the benefits of being associated with whatever Playtonic release, knowing what these guys are capable of, then that will be bitterly disappointing (for the guys at Playtonic as much as the fans, I'd imagine), and it will be totally Nintendo's loss.
Having said that, I'm sure we could all sympathise with Playtonic if they felt that Nintendo were asking for too much out of the partnership and the risk to lose control over the IP was too high, so fingers crossed, they can work something out!
(apologies for long post!!)