No reason (other than originality) that I know of. I've converted all the TRs I've owned to negative ground, and never regretted it.
If you don't have any aftermarket electronics, the process is simple. Disconnect the battery, swap the low tension wires at the coil and at the ammeter, reconnect the battery the other way. Repolarize the generator and you're good to go. All the other stuff (wiper, heater, starter, etc) doesn't care what polarity it gets.
Easy way to repolarize the generator is to pull off the wire from the 'F' terminal on the control box, and brush it against the 'A' terminal. You might see some small sparks, but they won't hurt anything. Then hook the wire back up to 'F' and start the engine.
But note that, if you go all LED, the turn flasher won't work correctly. You'll need to add dummy loads, or get a flasher designed for LEDs (which will have an extra wire to ground).
PS, almost forgot. If you have the original battery leads, you'll probably need to replace them. The positive and negative posts are slightly different sizes. Hasn't been an issue for me, as none of my battery cables were original.