[apache]

From what I recall, it already costs MPs to colonize, battle, most stellar manipulations, and lots of other things. As far as troop embarkment/debarkment, refueling, and other ship/ship or ship/planet transfers, I think its safe to assume some form of instantaneous star trek-ish beaming transport. But yes, troops should be confined to a planet for the rest of the turn if they were landed in a battle. There are also limits on minelaying, so I don't know why you are arguing that point.
Also, while this is a nice subject to debate, I would never post anything decrying "realism" here since the game pretty much ignores most laws of physics.