For the most part I agree with Nintendo, it it's too much of a pain I rarely chase achievements in games, it all depends on how far out of my way I have to go. The point that I think they are missing is that acheivements are a way of documenting accomplishments though, and a way for one gamer to prove that they actually did something to another, rather than just making claims through word of mouth and so on. "Acheivement or it didn't happen" is a common comment in certain gaming circles for this reason, as achievements and gamer profiles are a way of checking to see who is BSing or not.
Of course this also means that bugged Achievements are very annoying. For example I was with the second guild to ever kill Illidan on my server back during "Burning Crusade", when they added the Acheivement system I didn't get credit for this because I neither won loot from the final boss, nor completed the quest chain (due to real life scheduling and using all of my playtime either raiding or farming in order to raid), thus I am incapable of proving that I accomplished this, which is annoying.
The above is pretty much the only real purpose served by the Acheivement system, and I don't see it as a bad thing even if my "on the go" gaming habits have lead to me probably boosting more people's profiles than my own at various times. Truthfully, I think the future of the gaming culture is going to be to create some kind of universal gaming database. Truthfully I've been of the opinion that all of this would matter more if Sony and Microsoft and various PC game developers/services were to put aside their rivalries to create a linked system that would benefit them all. Sort of like how DC and Marvel comics fight like cats and dogs, but still get together to do crossovers for the fans, the whole "Amalgam Universe" thing of years ago showing what can happen when rivals can put aside business for the sake of the product and the fans.
Now I WILL mention an important exception here, which I also think is an important part of the evolution of the system:
A number of games provide tangible, in-game rewards for obtaining Achievements. The original "Mass Effect" for example gives you buffs based on the achievements you earn, "Champions Online" has costume piece and clickable power/item unlocks for certain "grind" based achievements (at killing 1,000 and 5,000 members of an enemy faction) ot to mention titles. "DC Universe Online" has perhaps the best system where Acheivement hunting is connected to alternate advancement and for every 100 Acheivement points you gain an extra skill point, this makes acheivement hunting a direct part of character advancement above and beyond simply grinding for exps, and hunting for item upgrades. I really like that system to be honest.
Truthfully I think that since Acheivements can be linked into the play of games themselves, that this is what more companies should be doing... make them an integral part of the game itself by rewarding players in the game for performing difficult (or at least time consuming) feats. That kind of thing tends to motivate me more than just getting a little stamp and a couple of points added to a profile.