My suggestion is to make any movement made to a square adjacent to a friendly planet FROM another square adjacent to a friendly planet completely free, with no movement cost. This would not apply to attacks... attacks would still eat up movement points.
This seems a little radical, but consider the fact that it is already possible with current game mechanics! If you send a ship to a planet, the move that puts them in orbit doesn't count against their movement limit. However, in the same turn you may change the planet's exit direction and launch the ship, effectively moving it as far as two parsecs at zero cost. This is a huge boon to defense and travel within your own territory, and allows for a string of planets seperated only by 1 square each to be a formiddable defensive position if you have the firepower to back it up. It makes the in game landscape more interesting... if you're willing to micromanage to gain that advantage.
In effect, all I'm asking for is the reduction of micromanagement for this unintentional (yet interesting!) game mechanic, since there is no functional difference for the player between free movement zones as such and the current orbit/launch combination.
However, automating the process has other benefits! For one, the AI now gets this strategy for free as it's built straight into the pathfinding, which makes the mechanic less exploitive of the AI.
Defending civilisations also get a sort of passive territorial bonus to their defense, slowing down their opponents and giving them a chance to more effectively fight back against opponents who would otherwise just crawl all over their space while rienforcements attempted to get in range. Likewise, attackers would be focused towards the front lines, where their free movement zones end and their opponents begin.
Another benefit is the "right of passage" treaties that were being considered before the betas could make their return. A right of passage treaty could gain you access to the free movement zones of another civilisation, giving you a faster way through their territory. This avoids the problems of earlier designs of the treaty, which would have slowed down passage through other race's territory dramatically.