Light falloff problems can usually be remedied. First, define the light falloff. With a 35mm carrier with a blank piece of film (clear, little density) in place and focused on the baseboard, expose a sheet of paper to a mid-gray. Then compare that to an exposure of a step tablet, to determine how much light falloff, in stops, occurs at various points on the paper. And do this a various apertures.
I personally wouldnt worry if the light falloff is less than ½ stop at 5.6. If more, you can probably modify the enlarger (clean the diffusion box, or condensers, etc). What type of enlarger are we talking about?
Finally, the Nikkor 50/2.8 is a great lens. I would only consider an APO lens if I were doing critical color work.