The 5-speed clutch might wear out a little quicker, and there are of course more parts in the tranny, but I would always buy that first all other things being about equal. Some heavy loader operators might want the 4-speed for the tougher clutch, but for general all-around work the 5 speed is better.
Also, 6 volt doesn't bother me at all, I'm not really even sure why everyone is obsessed with converting. I run a small farm in southern MN, I have 4 old gas 6-volt tractors I use, just took a generator in today to be rebuilt. 6-volt works fine if you keep the system up & run them once in a while. Grounding is important on a 12 volt system, quadrouple so on a 6 volt, keep that path good & it should work fine. I'd rather spend my money on a good plug in 6/12 booser/charger than to convert all the charging/ lights set-up on the tractor.
Now, if you need 12 volts to run something then I understand....