1) I'm operating under the assumption that the costs of developing the Wii U Gamepad & connectivity between it and the system was a relatively costly endeavor. Google search puts PS4 at a $384 cost of production, i'm guessing Nintendo could probably get to a fairly competitive price point.
I was under the impression that $384 was the estimated cost of PS4's collective components at launch which didn't include things like manufacturing. Therefore, Sony wasn't losing $16. Comparatively, Wii U's components cost roughly $230 at launch (the GamePad clocked in at a little under $80 of that sum). Nintendo was losing money on at least the Basic Set and probably less than Sony per unit sold. All hardware requires research and development so I don't know how much more costly it was for Nintendo.
2) If Nintendo's system would be nearly the same as PS4/Xbox One, what would really stop 3rd parties from doing what they do with the Xbox One/PS4, which is develop it primarily on one and port it to the other? Most articles i've read is that the systems are different enough between the specs and gamepad that it makes no sense to port them. Assuming they all started out the gate with similar specs/control schemes/limited technichal differences, doesn't this lower the barrier to entry for development on the Wii U and invite more ports?
In a vacuum, nothing is stopping third parties from supporting Wii U. Third support involves far more than just hardware. In fact, hardware isn't really an issue. Notice that many third parties are still supporting PS3 and Xbox 360. Some third parties are scaling their games. Metal Gear Solid V: The Phantom Pain uses the same engine across PS3, Xbox 360, PS4, Xbox One, and PC. Other third parties contract developers to handle ports either by scaling or just building assets specifically for older hardware. Apparently, Wii U hardware is close enough Xbox 360 in terms of architecture that porting shouldn't be a problem. Third parties are actively choosing not to port. There are a great many things Nintendo is just not doing. Paying for support and/or subsidizing development with upfront payments is one. General basic courtesies that Soren touched on is another. It doesn't stop there either.
3) Educate me on this one - what in itself is bad about Nintendo's online policy?
Nintendo doesn't (or refuses to) offer the same online features as Sony and Microsoft. For example, Wii U doesn't include universal voice chat. If you've seen voice chat in Wii U games, third parties had to include that themselves. Nintendo Network and the eshop are vastly superior to Nintendo's previous efforts (sadly), but neither are really where they need to be.