Vyor, I wish I could up-vote you more. What you said, I couldn't have said better, so I shall tag my thoughts behind yours.
The power-beam in Star-made allows for a sort of hybrid system. What if a small-ship with an individual jump drive, but without the power to drive it were to park in a major power-delivery beam. This would give you almost the "jump gate" dynamic but without the need for a second mechanism.
The other thing is that I don't want us to fall into the trap of arbitrary "small" and "large" categorization for ships. Let math do the categorization for us. If we define the power requirement for the jump based on a linear function like the sum of the dimensions, meanwhile the volume of the ship for power generation purposes expands on the cube. That should give you a natural threshold for warp capability, settable at the server level. But there is more we could do to affect game balance in some interesting and even plausible ways.
Proximity to a star system could affect such jumps. The bigger the ship, the "flatter" space has to be to jump safely. The larger the ship and the closer to a star, the greater the amount of random block damage on departure and arrival. This would deter Uber-carriers from suddenly (and rudely) appearing over peaceful planets. Damage-free jumps would only be possible in void sectors. Or if not damage, perhaps the energy cost goes up exponentially as you get closer to a star.
Jump cost in power could also be a function of the distance jumped. This might allow a medium sized ship to achieve short jumps of a sector or so to the next planet, even if they couldn't make it to the next star system.
With the addition of FTL, I imagine the universe should change a lot. Stars should be much more sparse in general, but with regular binaries and stelar clusters. Exploration would take on real meaning as we discovered the best travel-routes between locations, and discovered strategic trade-routes and mining corridors. At the moment if you have obnoxious neighbors, just move 100 sectors away and set up shop. There are just as many stars and planets there as anywhere else. But if you have a cluster of 5 stars nicely situated in a void between friendly factions... Now you have something to hold on to.