I think the problem with 3rd party games on Wii is really two fold.
(1) AAA games from AAA developers for the most part aren't going to the system, and never have been. Now we do have a few high profile counter examples (MH3, DQX), but we've never really had a situation like this, where the overwhelming market leader doesn't get the overwhelming market support. What Wii seems to to attract is largely B-tier brands, spinoffs, shovelware and niche games, the games are generally badly or unpromoted and budgets are generally lower than even last gen on PS2/Xbox/GC. It's bizarre, and even stuff like viable PSP ports that would likely do better on Wii (Soulcalibur BD, Kingdom Hearts BBS, etc) aren't materializing. It's like the industry wants Wii to fail, like publishers are actually fighting the will of the marketplace, and I'm honestly at a bit of a loss to explain it.
(2) Robust 3rd party support didn't come fast enough, and as such didn't build markets to support core oriented games as should be expected by the overwhelming market leader. I think Samurai Warriors 3 makes a great example of this... the game sold over 250k in Japan, which evidently didn't hit Koei's expectations for such a high profile release, but the real issue here was that they'd already built that Musou audience on PSP/PS3, and this was Wii's first legitimate Musou game coming a full 3 years after launch. By comparison PSP got it's first Musou at launch (and it also sold around 250k), PS3 got it's first Musou less than six month after launch (sold 300k and carried the popular Gundam license) and even 360 got it's first Musou less than a year after launch (it bombed but well... it's 360 in Japan). The problem here wasn't that Koei bothered with Musou on Wii, the problem was that they did it 2-3 years late... and really this story is emblematic of 3rd party Wii games. You look at the first year and we saw quite a few notable 3rd party success stories (Red Steel, COD3, RE4, REUC, DQ Swords, Sonic SR, etc), but that wasn't really followed up on or supported fast, frequently or just well enough. I think to some degree that market got tired of waiting and moved on. And honestly, this problem may be more of a "too late" situation, the only question in my mind is if 3rd parties will fall asleep at the wheel and make the same mistake next generation...
