Studying both MMA and Aikido in the traditional sense, I can tell you I think there is room for traditional martial arts such as aikido, I think it is relevant as practiced, I also think that there is much to be learned from other methodolgies such as MMA.
Aikido, like any budo, has an omote and an ura. There's been a lot of valuable philosophical exploration of the ura. However, if we lose the omote, the whole thing disintegrates. You can't have one or the other. I'm not sure you can even really -emphasize- one or the other.
I think MMA -is- a wakeup call. Not a challenger "we" need to fight and defeat - frankly, not only would that be wrongheaded, but furthermore "they" would win. But I think that hiding in a cave muttering that "we do REAL fighting, not that sport stuff!" is senseless. What IS aikido's intended context? And whatever it is, shouldn't it translate at least somewhat into MMA-style situations?
It seems like most great aikidoka, past and present, have also been skilled in other martial arts. Coincidence?