It's really no secret that Nintendo games tend to go up in value shortly after launch, and sometimes they can even become rare. The Wii U is no exception in this regard, as it has already accumulated a handful of games that have shot up in price and are hard to find, with more on the way that could potentially follow suit.
Current Rare Games:
Pikmin 3 is quite possibly the most high-profile Wii U game that is hard to find. It's currently $76.99 on Amazon US, and unless Nintendo releases a 'Nintendo Selects' edition of it in the future, it's looking unlikely that it will go down anytime soon. If you're a fan of this series or genre, it would be wise to keep an eye out for it before it goes up any higher.
Unusually, this 3rd party collaboration with TT Fusion is quite possibly the only Lego game to ever become rare. It sits at $64.49 on Amazon US, randomly booming in price recently despite being on the market for over 2 years.
Wii Party U sold quite well, mostly due to being bundled in Japan, yet it has become fairly rare regardless. The version of the game that is bundled with the Wii Remote Plus is currently $69.99 on Amazon US, with the regular edition pretty much nonexistent in most stores.
One of the early 3rd party releases on the Wii U, Warriors Orochi 3 Hyper is part of the niche Warriors series, so it's no surprise that it didn't sell too hot, which could be a reason why it's now $63.99 on Amazon US. Who knows though.
Wii Sports Club is essentially an HD remake of the original Wii Sports, with added features and an additional sport. The physical release of the game is certainly not common in stores, and it costs $59.73 on Amazon US.
Potential Rare Games:
Developed by Yuji Naka and published by NISA, Rodea The Sky Soldier is an upcoming third-person action game for the Wii U. The first-print edition comes with a physical copy of the Wii version of the game, and I fully expect both that and the normal edition to become rarities in the Wii U's library, due to its niche concept and inevitable low shipment.
Fatal Frame has never been a series known to fly off the shelves. No game in the series has sold over 250k, and it's not likely that Fatal Frame: Maiden of Black Water will be much different. If it does happen to get a physical release, I would jump on that as soon as possible, as I don't think Nintendo would supply retailers with a substantial shipment.
Bayonetta 2, unlike The Wonderful 101, has completely retained its value since launch. It still goes for $54.99 on Amazon US almost a year later, and I don't see it dropping too much anytime soon. The fact that it comes bundled with a physical copy of the original Bayonetta will make it a game sought after by collectors, and it's not likely that Nintendo will keep producing units of this game for a long time, making it a recipe for rarity.
Devil's Third is the first game developed by new studio Valhalla Games, run by Ninja Gaiden developer Tomonobu Itagaki. Given the fact that reviews will not be kind to this game and it's not quite in a mainstream genre, it's more than fair to say that this game will bomb at retail. I mean, it's retailer exclusive to Amazon in Japan for crying out loud. I don't see many physical copies of this game being shipped, so I would keep an eye out for it (if you're interested, anyway).
Genei Ibun Roku #FE (Illusory Revelations #FE), original known as Shin Megami Tensei x Fire Emblem, is an upcoming JRPG for the Wii U. Although this game does have the potential to sell quite a few copies, I don't believe that will diminish its value. Fire Emblem games more often than not go up in value after release, and I don't expect Nintendo to treat this game any differently. Especially since it's on the Wii U.
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Of course, there are quite a few more games out now on the console that are rare, and I believe more than I listed will be rare in the future, but I think my list gives a general gist of things. The Wii U is a system with a relatively small library, but its value will only go up as time goes on.
