Some factions, including minor ones, particularly those which are militaristic, could be able to research tech which allows their smaller ships to be able to attack ships which are jumping between star systems. 


It could either be an actual battle or just a raiding tactic, and would have a failure chance as well so as not to be over-powered.


Alternatively you could set up pillaging routes, whereby you can set a fleet to raid a group of systems sequentially.