Having now played the game a grand total of two times, with 1 loss and 1 win, some will probably say that I lack sufficient experience to really comment on this issue, but I am a 25-odd year veteran wargamer I do think that my experience overall is of value.
I think that ShopKeepJon has very eloquently summed up the salient points in this discussion, but there is further point I'd like to add.
Essentially, as I've played it (and seen it played), the boresight and initiative game mechanics can be made to work together such that the game mechanics themselves determine tactics rather than any actual strategy you may have planned.
IMHO, this is generally undesirable, since in a perfect gaming system (and there are none!), the game mechanics should essentially be invisible at a tactical level.
Consider the following example:
1 G'Quan facing off against 1 Omega in open space.
Tactical maneuvering aside for one moment, both of these vessels will be looking to boresight each other with their main weaponry, and the initiative system will generally support this invisibly - whomever wins initiative is likely to be able to get a boresight on their opponent, at least until they've closed to well within range of secondary weapons systems.
So, if the G'Quan consistently wins initiative, the Omega will probably never get their main beam to fire, but this is precisely correct since clearly the captain of the G'Quan has outmaneuvered his opponent.
Now, throw in a Hermes some 50" away from the main action, that never does anything other than an "All Stop" SA. Suddenly, no matter how good the G'Quan captain is, he'll never be able to outmaneuver the Omega and get his boresight to bear, because no matter how well he rolls initiative he'll always move before Omega (assuming the EA player isn't an idiot anyway!

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Now the G'Quan is really left with two options:
1. Close into secondary range with the Omega, which probably isn't a good idea since the Omega has longer ranged secondaries and interceptors.
2. Turn to destroy the Hermes. This is probably easier said than done though since the G'Quan is slow and lumbering - it's likely that the Omegas main beam will have finished it off long before it's even turned to face the Hermes, let alone got within range.
The point here is that the Hermes does not pose a significant threat to the G'Quan. at least compared to the Omega, yet it is having a very significant impact on the tactics of the G'Quan. This is not due to any capability of the ship (it is far to far away to be of any consequence), but due to the boresight and initiative game mechanics.
If this were a real-life situation, the captain of the G'Quan would ignore the Hermes entirely and concentrate on the Omega, but the game mechanics do not allow this.
I'm sure someone will want to say that the G'Quan captain was "out-thought" by the EA fleet, and should've taken out the Hermes earlier in the game, but for the basis of this example we'll assume that the Hermes jumped in from Hyperspace whilst the "end-game" was being played out!
Now I know that this is an abstract game, and as such you will almost inevitably be able to find examples where the abstraction breaks down, and I also agree that these won't generally spoil your enjoyment of the game as such examples should turn up relatively rarely.
However, there are sufficient voices on this forum that believe that this particular issue is a problem and would like to see it addressed. I'd probably consider it more of an "artifact" than a problem per se, but I do see and recognize the issue!
As to potential "fixes", one I'd like to throw into the mix which I hope hasn't been kicked around before would be to allow the initiative winner to always reserve one ship to move last.
At present, winning initiative is supposed to give you a tactical advantage but in the example I posited earlier, winning initiative will do nothing for the Narn player, since the Omega could always move last as long as the Hermes was still in existence. If winning initiative allowed the Narn player to reserve a single ship to move last, the tactical advantage of winning initiative would be restored.
Regards,
Dave