Obviously, the slower lens will usually have better bokeh. People have complained about the out-of-focus highlights with the 50/1.4 (all versions). I haven't been bothered by them, though. The only lens I didn't care for out of the 50/1.4 series was the SC version. It had low contrast, compared to the S, the AI, and AIS versions (as well as the AF/AF-D versions).
Between the two, the 50/2 will have a little bit of an edge. But, if you need the extra stop of light, then go ahead and get the 50/1.4 Nikkor-S. The 50/2 late non-AI and AI lenses do focus a little closer than the 50/1.4 S and the 50/2 H. They are also a bit smaller and lighter. It is possible to slide an FM2n (or an FM) with a 50/2 mounted into one of the sections of a Domke F-2's standard 4-section divider insert, though. Whereas, with the 50/1.4, it'll be a tight squeeze.