However this number includes the bundled copies wich don't make Nintendo any additional money.

No it's not.

R&D

Nintendo's projections were based on high sales (Wii level sales actually) so all those calculations are worthless now with sales so low.

Lower sales lead to higher production costs per unit than projected. Also, things like marketing budgets are fixed so the marketing budget stays the same but profits from sales are lower than projected. And of course work force, warehouses, development costs, etc. are fixed costs too. Nintendo's fixed costs didn't decrease but revenue from sales decreased a lot. For instance if 2m customers bought a Wii U + Pikmin + Wario that would've made them a profit. But if only 500k people buy the same combo Nintendo bleeds money because Pikmin 3 needs to sell more than 500k units to cover its dev costs.

ah ok thx for the explanation.

There really is no telling how being off projected shipments that badly has hurt Nintendo. From what I gather, Nintendo shipped a minuscule amount of Wii U units last quarter because stock level at retail was still very high. What kind of stock are they holding in storage? I would imagine that they spent a lot of money on production set-up with Foxconn but how much have they had to scale back? You know that they can't be running the same kind of schedule, which greatly impacts efficiency. It has to be a huge mess on the production end, given their early projections and goals.

As CavemanCavan said above, the more you manufacture, the cheaper your production costs are per unit. The same is true with your front-end costs, like advertising and shipping. The Wii U has been so far off Nintendo's expectations that there really is no guesstimating how it stands with regards to profitability. Only Nintendo would know for sure. However, I think whatever time-frame they had initially is out the window.

Its the same situation with Sony game division at the moment though.

Massive lossed despite the PS3 selling incredibly well, though the Vita is underperforming.

Its because of recent R&D Costs for all the big 3

No it's not. Sony has big R&D costs because the PS4 is yet to be released, the Wii-U has been released a long time ago. Sure Nintendo have a big amount of games in development but it's in no way comparable to the release of a system.

But the amount of R&D money that goes into a console in its first year of release is huge.

There has to be funding for bug fixes, any extra infrastructure needed to support any online services, updates to features and the development and testing of new features.

It is not just spend the money then release it, it continues for a long time.

I agree with you that Nintendo is spending a huge amount on R&D, but i was responding to you saying that the situation is the same as Sony's. Sony is currently in the process of releasing a new system, and with that producing a few million PS4's. That means building up stock without these devices currently being on the market. That's a way more expensive process than Nintendo is in, Nintendo is already past that point.

True, but even still R&D costs would be higher before launch than after launch, yeah there are bug fixes and feature updates after launch, but nothing compared to what they'd currently be going through pre-launch during internal testing and development. And online service infrastructure needs to be stood up before launch to handle the surge in use on launch day (when everyone picks up their shiny PS4's and connects to the PSN). So though there is elevated R&D costs after launch, I'd still contend that they would be lower than pre-launch. 

As for Nintendo's 2 games to profitability statement regarding Wii-U, as others have said that would have been assuming sales were in line with their projection at the start. Given they are far below that, all their fixed costs are spread over fewer consoles/game sales, and therefore they need a higher number of console/game sales to compensate. Not that they won't get there soon, but from the wording they used during their last financial statement they aren't there yet.