For game mechanics, consider if all your players are on the same timeline or not. If there's a big difference between interstellar transit time and travel-time to what your system uses for jump points, you can't have players A&B making three transits of 10 days out to safe distance from star (or to the nearest wormhole or to the spot where physics permits folding - whatever) plus 10 minutes (or 10 months) in FTL, whilst players C goes to the same place with one jump... If everybody's in the same sequence of events, there's no problem with a turn or unit of game time to be the same for the 10 days as for the 10 min or 10 months. A stretchy, rubber clock, if you will.
If you intend for players to be jumping hither and yon across a galaxy, and interacting in real time, pick an FTL system that matches your needs. Like others mentioned above, maybe the constraints are how much energy you have to spend, or how big a ship you can use. Or how much unobtanium your ship has in its tanks :-). But it always takes one turn or two turns to transit - something nice and simple.
If you don't want players to get dropped from the game by the delightful problems others mentioned above (You have arrived at a dead end with no exit. Good bye. Go get the rest of us some pizza.) then maybe make all your interstellar travel from predefined transit points, and leave the "Galactic Engineer Corps" and their slow/expensive/catastrophic initial placement of gates/wormholes/fold points off-board and out of play.
If you want to force some decisions and tradeoffs, set some kind of parameter like big ships make the transit point unusable longer than small ones. Or the same armor that makes ship A well-nigh invulnerable causes a percent chance of a random alternate destination instead of the one you planned <evil grin>. Ship B uses shields instead, not protecting from thermoplasmic disruptor lances as well, but actually enhancing ship integrity in warp space (pick your own technobabble).
Exploration & battle both, eh? Do you intend to have a mapped-out sector to work in, or will someone's decision to "head 500 light years thataway" automatically leave him somewhere interesting and useful? Are you going to severely limit the number of possible destinations, like Cherryh's Chanur or Alliance/Union universe? Is there a gamemaster, or does everybody play? If no gamemaster, are you going to rig something random to set the characteristics of places before they're explored? Maybe picture a Settlers of Catan board of randomly placed hexes, with players only turning them over when they get to them. Or a set of Battleship boards so each player has their own secret map, and they annotate it or stick in pegs or whatever to match their own unique knowledge - the aforementioned hexes stay face down the whole game with players getting a peek at their characteristics when they get there. Or a mixture - some predetermined ones are "already mapped" and common knowledge. Or a player needing money (energy, mana, supplies, fuel) could trade knowledge of places he's been "to the community" and publishes it to the Atlas Galactica by turning over one or more hexes so all can see from then on. Hey, that sounds interesting - if you don't try something like that maybe I can work up something to do with my Catan games' hex tiles :-).
Or how about a map system a little like that of Nexus Ops - semirandomly preplaced hexes where the different terrain is visible, but some token or characteristic has to be 'explored' to find - a mine or a new unit, in Nexus. Interstellar "terrain" could be what, observable characteristics of stars? Rudimentary data found in the Travellers' Guide to the Link Network, recently translated from the ancient language of the link builders... but some things aren't known until you get there - is there a local civilization with gas stations and recreational facilities? Did the star go nova since the guidebook was written, and there's nothing of interest there?