Black Ops 2 doesn't have Elite
at launch, neither does the PC SKU. Doesn't mean that the PC has a crap online infrastructure, does it..? And doesn't that mean paying a years subscription anyway..? The online infrastructure will be fine, Miiverse in particular is going to be
huge. If there's any one of the three platform holders that can take on the likes of Facebook and Twitter, it's Nintendo.
Third parties have had a great deal of input into the online infrastructure and I don't think there's been a single developer complaining about it so they must be doing something right.
As for Nintendo's first party titles having online play I can't see it being any use for any of them apart from Mario Kart as you've mentioned...but I'd much prefer the likes of 3D Mario, Metroid and Zelda - the Nintendo IPs I'm most interested in - to be single player experiences anyway.
The only Nintendo game I want to see online play integrated into would be the next Wii Sports. Bowling and Golf would be great having online play. We'll have to wait and see I guess, although Nintendo are really pushing this asymmetric multiplayer so we may not see it.
And FIFA not having Ultimate Team has nothing to do with the online infrastructure and everything to do with the fact that it's a launch title. The pressure involved in releasing a launch title is unbelievable, mainly hampered by a new set of unfamiliar standards (in this case Lot Checks) and the fact that dev kits and SDKs are being changed every five minutes. It's a bloody nightmare, particularly if you're a lead tester.
We may see online play integrated with Retro's new game if they're not working on a Metroid game, if Nintendo have any sense they'll be working on a new TPS or FPS IP aimed at the Western market.