If we're talking about patching Jomon, one thing I'd really like to see is the Ninjas made a little better. They should at least be able to take out a generic indy commander without the use of magic items... given that the more common 'Assassin' can do this without difficulty.
They can. I played using large amounts of ninja in one game and had a fairly high rate of success taking out non-mounted indy commanders. Mounted ones were rather a lot harder though. I may or may not have been using only ninja with one experience star plus though.