Hmm, what if jumpships were not allowed on any planet higher than their mark? So:
mkI jumpships are for internal redeployment only.
mkII jumpships can get around pretty well, but are often restricted.
And so on, with the HWs only accessible to mkV jumpships.
(all human-controlled planets are treated as mkI).
This also gives incentives to actually build the higher-mark jumpships.
Edit: chokepointing problems.... I don't think it would be that bad for most maps. (stuff like maze, snake, tree, ect. are out of luck, but I don't see a problem with one specific type of Spirecraft having it's effectiveness determined by the map, especially as the relative power of other spirecraft (attritioners, for example, are much better at single chokepoint setups) should increase.)