I do kind of like the idea of having both. Gates and jumps can both have a place in gameplay - the way that I usually see things done is like emsreaper mentioned: gates are typically used by smaller ships that aren't large/powerful enough to mount jump drives, while jump drives are used by large, powerful ships that are often too large to fit through gates. (Sometimes, gates are also used for travelling very large distances for which it would be infeasible to use a jump drive.)
Both ideas can be balanced through various means - the tradeoff for a jump drive would almost certainly be power draw - I like the idea of power requirements/charge times changing depending on the length of the jump - and the ship would likely not be able to fight at full efficiency until the power cores had time to recharge. Gates would likely be easier to set up, but they could also require their own dedicated power source to operate/recharge, with recharge times increasing with the number of generators. They could also require more power depending on how far away their corresponding gate is. (Maybe they could be more energy efficient than jump drives?) Maybe they could also be switched to jump to different gates on the fly, so that it would be possible to build hub gates that connect to many different systems!
There are certainly a lot of possibilities, for both ideas. Perhaps it could also be possible to customize the size and shape of gates using blocks (like a frame of some sort), and require larger amounts of power to operate larger gates? Perhaps jump drives could function like shields, where grouping them together would essentially give you a bubble in which everything is teleported. (This would definitely require balancing, however - such a tool could be quite dangerous! It could have possibilities for mining and other related uses, however.) Perhaps they could instead teleport everything that is connected to them, requiring larger amounts of power for larger numbers of blocks. Imagine, it could be possible to jump entire space stations or asteroids - the uses are potentially endless!
Personally, if there's anything I'd like to see, it would be a jump drive similar to the one featured in Evochron Mercenary, where you could input specific coordinates to make very precise jumps. (I.E. a specific space station, asteroid, planet, etc within a system, instead of just jumping into the middle of a system.)
Anyways, it's important to remain open-minded! We don't necessarily have to use only one method or another - if done right, we could get the best of both worlds, and have some truly refined systems for travelling across the galaxy!