1) You get ECC memory and can opt for a Xeon CPU which multi tasks way better than Core versions in my experience. (NUC is space constrained so less thermal headroom thus slower sustained performance and the need for a noisier fan.)
2) Substantially better build quality - for added benefit my tower z230 sounds much quieter than the NUC which I have to keep on the desk.
3)The prices are not that higher than the fully loaded NUC for the features you get - for example $787 for 256GB SSD, 16GB ECC RAM, 1TB disk latest Xeon E3 and GPU built in.
4) I am not sure if you want RAID for data protection but sounds like you are careful - so the workstation I mentioned above gets you 5 disk bays - one SSD and 4xRAID is great to have. Not an option with the NUC.
5) It comes with a Windows license unlike the NUC and you get a Enterprise grade warranty for a year which you can extend for very reasonable price.
I am constantly delighted by my Z230 - it is fast, reliable and allows me to multi task quite heavily without any slowdowns.
My current laptop (running Linux), which certainly doesn't have ECC, hasn't had a system crash since I've had it, which is well over a year. In my experience system crashes with properly working software and hardware should be exceedingly rare, even without ECC. Granted none of my machines have had 32 GB of RAM, my current laptop has 8 GB, but that's only a factor of 4 difference and I'm pretty sure my accumulated experience with various machines adds up to far less than 1 unexplained system crash per month per 32 GB.
But in our customer support everybody has a Nuc and they're running fine, I was the only one with these problems.
Probably I'm just unlucky.