I have the actual nifty fifty, the 50mm 1.8, and the 40mm. I don't have the 6d but that is my upgrade kit, so here is what you might want to consider. The nifty fifty and shorty forty are very similar. Both are small, lightweight, inexpensive. The 40 is a little slower at 2.8, but stellar wide open, and good for almost-macro type shots with a close focusing distance. The 50 is wider aperture with less depth of field, but older, cheaper, and little iffier on autofocus abilities or macro.
If you are really looking at the 50mm 1.4, you might want to wait and see what happens with the upgraded 50mm IS that will be coming out soon (following in the footsteps of the 24, 28, and 35s). I think that lens could coexist nicely with the 40mm.
If it was me, I'd pick the 40mm now and wait on the upgraded 50mm. When I bought my nifty fifty, there was no 40mm and no IS primes on the horizon, either. Shoot with the zoom and the 40 for a while, and decide if you would rather have a wide angle prime, a normal prime, both, neither, etc. But the pancake will always have a spot in the bag due to its size and quality.