You could undercut the gears of the transmission while you're in there. You can do it yourself, there's tutorials floating around, or there's people out there that will do it for you via mail. Done well it really sharpens up shift action, especially for older bikes.
If it's a high miles motor, or the compression is down a bit it's not that much extra work to hone the cylinders and re-ring the pistons once the cases are split.
You might check with a bike specific forum if there were any known issues/gremlins lurking inside you can fix while you're there, but otherwise if it was a strong runner before, no need to fix what isn't broken. The only other thing I could think of is that setting the valves would be easier and less tedious with the engine out of the bike.
