Why is crystallography still used in some cases for small molecule structure determination?
Our group uses both methods a lot so here are some examples why you would use X-ray, in addition to NMR, in organic synthesis.



Your compound isn't soluble enough:

Colleagues produce very large aromatic systems for organic electronics which are basically insoluble in all solvents. With a good NMR machine (600MHz and up) it might still be enough to get spectra, but full structure elucidation might be difficult. Since the compounds crystallize well it's quite easy to get a X-ray structure.



Low number of carbon and hydrogen:

I've produced compounds with a C:H:N ratio of 2:3:5. The 1H is two singlets, the 13C is two signals. COSY, HSQC, HMBC,... won't tell you much either and it's much easier to use the nice crystals and get a structure that way than trying some correlated NMR experiments including nitrogen.



3-D orientation/stereochemistry:

Imagine this compound which is quite similar to something we produced:



Since you got two quaternary centers here it's really hard to tell the configuration on those centers relative to each other using NMR. There's no coupling to determine the stereochemistry and a NOE experiment isn't very conclusive here. With X-Ray it's no problem to find out.

Actually, these problems are definitely the ones we use X-ray the most.



Absolute Configuration:

Theoretically it's also possible to determine absolute configuration with single crystal X-ray diffraction, while it's extremely hard to do, if not impossible, with NMR.



Summary:

Single crystal X-ray diffraction gives you the configuration of your molecule, including relative configuration of stereocenters and possibly even absolute configuration, right away. If you only care about configuration (and not behaviour in solution) X-ray is definitely superior to NMR, there's basically no question on how your molecule looks.

On the other hand you need crystals and it's much more complicated to perform than NMR, so this definitely stays the number 1 method for synthetic chemists.