I'd always thought that EVE had a neat idea about deep travel with Cynosural fields. One ship acts as a beacon so that capital ships can warp to the location.
Maybe you could have a capturable alien technology, like golems, that act as 'warp gates'. There are two ships, and both must be found in the map. One ship acts as the exit, another acts as the entrance. The entrance ship emits a field, that when activated, transports all ships within the field radius to the exit ship. Counterpoints could include being very weak, massive energy usage, limit of jump distance, delay before transported ships can move and extremely long recharge time.