AT's Star Trek mod has good supply system. The faster your ships move, the more supply (over what they regenerate) they use. It goes by tech level too, so you won't be crossing a system early in the game.
One of the principles of 4x games is tech. Do you want to move fast or shoot at somebody? Your tech develepoment is crucial and must be uniform over what your intent is. Supply and supply related techs should be included.
A system that uses supply points such as bases or depots also creates places of engagement other then planets. Not all planets would be supply points, but could build a ground/orbital base to resupply ships. Supply routes to these planets/bases should be determined by a ZOC and abstracted for those who do not wish to command every supply freighter in their empire!
Just a few thoughts...

cause I don't get many of them!!!
