I personally think that the best solution is sort of what \'S-Guy\" said, and very similar to the series \"The Lost Fleet\". The gates would function as major, important pieces of the Galactic \'market\'. The warp feature should be enabled on every ship, but have minimum requirements, such that there is an unofficial minimum ship size (therefore rewarding players that are clever enough to compact the systems onto an even smaller ship).
In more depth:
---WARP JUMP---
There should be a maximum distance that you can travel with these (such as maybe 5 sectors, like someone already mentioned?). In order to encourage more professions, one can also make it so that more advanced warp drives are craftable, but cannot be sold to shops, nor can they be bought from shops. These \'newer\' cores would also have the ability to be \'enhanced\' so that they are slightly more energy efficient, or have a slightly shorter cooldown, or activation time, etc. The drawback to these is that ONLY players can craft them (they would be expensive to craft), and, since they cannot be acquired from shops, ships that have them as part of their blueprint would not recieve them. In effect, this makes it so that if someone had a powerful warp core, they would think VERY carefully before doing anything silly with it, for fear of losing it. (Of course, once the economy becomes more fleshed out, losing a ship in general would be very expensive, and not something anyone would take lightly).
---GATES---
Before I say anything here, I want to point out a MAJOR issue that no one here has yet addressed. Say I have a gate of a certain size at my faction base, and want to transport a large ship to another gate, say near a marketplace. Although this situation may be somewhat unlikely, it can definitely happen unless more constraints are applied. If I pilot my ship through my large gate, but the recieving gate is too small, what happens?
The best solution I can come up with for that problem is to force all gates to have set dimensions, (like 5x5, 7x7, 9x9 etc). Another solution, although I don\'t know if it is any better, would be to inform the player, prior to your own gate\'s activation, the size of the recieving gate (thus forcing players to know the size of their ships :P ) and to let the player suffer any consequences with their choice.
As for gates in general, I think that they should be a lot faster (ie. instant) compared to the warp drives, and at least slightly more efficient (because they are stationary). However, you MUST have a \'key\' (be it a password or a physical item) for both the starting gate, and the destination gate. This enables both a form of protection so that people don\'t use gates they aren\'t supposed to, and can be VERY interesting for PvP. Imagine if the keys could not be reset once a gate was made....in faction warfare, if a spy ship could somehow sneak in and steal the key, it would be a vey valuable asset (This is the plot of \"The Lost Fleet\" series I previously mentioned). This would then force the \'defending\' faction to either: remake the gate, and redistribute the key to all of its subsiduaries (a large hassle), or catch that ship (a potentially dangerous scenario for all involved). Now if that ship can only go so fast, is unarmed, and can only jump so far/after a certain delay, the task is not nearly as difficult. But imagine the adventures one could have if that ship wasn\'t just a ship, but it was a small, stealthy, state-of-the-art fleet.
I know already that a large amount of people will be opposed to this idea, but I think that it is the \'best\' way of going about this, placing importance on both the warp drive as something not to be underestimated, but not something to be easily abused either, as well as making the gates a more \'dynamic\' issue. One does not simply place a gate at their base, and walk away, leaving it completely undefended.
Just something for everyone to ponder on,
-Proically