From my expirience with missiles in .87 my take on this is as follows:
The damage on missiles is nice; I have no problem with shield:hull ratios whatsoever.
Improved tracking on ammo weapons makes them reasonably effective in combat.
In my opinion the problem with missiles is their 1) Speed and 2) Refire
1) Having the ship speed added to the overall speed of missiles is good. Therefore I suggest nerfing the speed of the missiles to 2/3 or even 1/2.
2) Simply halve the refire of all missiles. Spamming becomes less effective, the dps is halved, aswell, and the other player has a reasonable amount of time to prepare for the next incoming missile.
Countering missiles relies heavily on reflexes and expirience - Predicting when a missile will be fired and knowing when to fire CD/CMs.
And, frankly, reflexes and expirience is not what I associate with the common discovery player. Therefore improving on this issue will fix the problem, imo.
Edit: I don't think missiles should have any kind of delay, it hinders gameplay in the same way lag did in .86.