riiiight, well i'll give my view of the matter
1. Will there be upgrades available, and will the improvement be speed related (ships go faster) or range related (ships go further, assuming range is an issue)
Definatly, has been officially confirmed by the devs, both on speed and range(ammount of Antimatter reserves). Range is also an issue, because the map is full 3d. There
might also be upgrades to jump deeper into gravity wells.
2. Can you (and if not it might be a good idea) order your ships to change course while they are in transit.
I sure hope so, i've asked elsewhere but it hasn't been answered (yet)
3. Can you impose countermeasures that stall enemy FTL drives when they enter your system, forcing them to go it at sublight.
unknown, it would be nice. We do know that ships will arrive some distance away from the planet.
4. Is it possible for your ships to deplete their fuel reserves during a jump and be forced to a) stop and recharge or 
be towed and/or refueled by another vessel.
Not during a jump, as there is no interplanetary space (between planets or solar systems) When exiting in a system/near a planet, it is possible for Antimatter to be depleted, which, parafrased, "makes shields less effective" and prevents use of abilities, as you need AM for these.
5. Finally, Phase Gates, do these consist of two gates with a stable link between them, or an anygate to anygate scenario, or can ships use on gate to increase speed (exiting through it without entering another one)
I personally agree with the discription given by mongoose, as it sure sounds like it. Keep in mind that the info in the ship section of the website is pretty old. If it still exists, I believe one should read it as "The ability for ships to jump directly to the scout using the ability, instead of arriving at the edge of the system. This ability also reduces AM useage of incoming ships"
The construction of a stargate like system (or even one or two way system) would prove a huge advantage and would certainly fit in with what we know of the lore.
The ability to jumps from A to D without having to stop and refuel in B and C will be a boon, but going from A to G is even better. Even if the range is limited, I see the construction of a massive gate network as a major boon. Having your enemy hit your gate nexus wouldn't be a pretty though.
