I agree that the determining the discount rate (cost of capital) can be pretty difficult in real estate. When I do the NPV analysis, I use discount rate as a rate I could probably earn on similar risky investment (ie. on financial markets). Even though it is not that exact, using CAPM (Capital Asset Pricing Model) as a discount rate didn't work much for real estate.
How are you guys determining the discount rate in your calculations?
In my opinion, if I keep my method of determining the discount rate consistent, I can still compare various properties (investments).
I also agree that NPV can't be the only measurement of an investment. The same thing is valid for IRR, though.
IRR doesn't take in account much the size of the initial investment needed. If there would be two investments, generating both 10% IRR, one can have initial investment of $10K and one $100K and you can't tell just from looking at IRR.
For this reason also Profitability Index is a good calculation, in my opinion.
Profitability index = (Present Value of Future cash flows) / Initial investment
Anyway, you are right as well that calculations is one thing, but then you have to access the investment with common sense and guts to make the final decision. However lot of "investors" are using just the guts and no calculations, which is bad as well.