THQ is turning their back on their legacy (Toy HeadQuarters) and stopped doing their licensed "kiddy" games. So if anything they grow distant from Nintendo.
Level 5 -- good point. They even have publishing agreements with Layton. And Inazuma Eleven is still big
N-Space -- these guys are just contractors, they will do what they're said by publisher, be it Activison or Square. Also they're pretty always big on nintendo handhelds mostly. They got themselves a niche of goto guys for big publisher to outsource handheld ports and doing okay for themselves i think. Nothing is really changed for them.
And again -- they're mostly handheld guys, so Wii U will do nothing for them.
Silicon Knights -- dead
Next Level Games, Monster Games -- nothing is really changed, they're already more or less second party.
Tecmo Koei -- they get closer with Nintendo with recent DoA, NG, Fatal Frame and Nobunaga releases, but actually mutual dependency and Nintendo needs them just as much.
Namco is going to slowly migrate their main profit source (all these countless anime licensed games) from PSP to 3DS. Smash Bros and Tekken with some occasional Tales of is probably all we we get.
Xseed and Atlus are super niche publishers. Their games are for dedicated audience who might have find no problem buying a console or handheld for just one game or super collector edition for 200$. They are very platform agnostic.
With 3DS dominating the japanese market for years to come and WiiU seemingly coming in force these holidays -- overall Nintendo grip on japanese third parties will be tightened. But this won't do much for western publishers who are waiting it out and are more inclined to jump on next xbox. But 3ds is a MUCH bigger factor here, so wiiu won't change much.
There are two western publishers who will be get more dependant on nintendo directly because of Wii U, though
1. Activision -- Skylanders are SUPER HOT and NFC on gamepad seems to be tailored for that kind of physical/videogame promotion. Wii was the leading platform for Skylanders (both in development phase and in sales) and that paid off in diamond spades. Also, BLOPS on Wii U launch will do some decent numbers (at least a million is a lock).
2. Ubisoft. They seem to found a new console to dump their ZZZ-games on -- they have like 10+ of their usual shovelware ready to launch. Just Dance, Rabbids, Assasin Creed should do fine. Rayman will do okay and will get ported to everything under the sun half a year later.