ScottieATF said:

How many times have you fired a Proton Torp and missed a tie entirely?  Homing missiles will at least let you ignore evade tokens, and the concussion missile will save you from rolling 3 blanks on your attack, but thats still 9 points worth of missiles.  Thats over half the price of adding a prototype A-Wing for maybe getting an extra hit on the table.   I think if you really want missiles to work, you want to run Horton, Wedge, and an A-Wing, and even then I'm not 100% sold on the missile on the A-Wing.  

If you're planning to use Green Squadron + Push the Limit, I think Concussion Missiles are a better choice than Homing Missiles. The damage distributions look very similar, and the expected number of hits differs by only 0.07 (3.68 for Concussion, 3.75 for Homing). Basically you'll never be able to tell the difference in play. 

The Homing Missiles have the advantage of preventing your opponent from spending Evade tokens, but I'm not sure that's worth the extra build point.

So I would run Green Squad + PtL + Concussion Missiles if that's where you're leaning, and use the extra points to beef up the Gold Squad pilots with generic astromechs. 

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An alternate idea, though, might help round out a possible problem with the list. In my experience ships with low pilot skill sometimes have trouble with missiles and torpedoes, because they have to have a Target Lock on an enemy ship--and getting a Target Lock on a ship that moves after you do can sometimes be a pain. (For instance, Vader is just out of range when the Greens move, and by the next combat round he's at Range 1 and/or out of their firing arc.)

One solution to that problem would be to use Deadeye + Homing Missiles. That way your A-wings can target any ship that's within range when they fire, rather than when they end their movement--and you still have four dice with Focus. It is a step down from the Push the Limit combos, and you also don't benefit from having Push the Limit after the missiles are away, which is a shame because it's a nice way to wring a little bit of extra offense out of the A-wing. But it's an option.

The generic base ships are still very attractive buys in both factions.  I don't think the Green Squadron pilot will be left wanting for at least a few ships tha will be forced to move before it.  Yes it puts Vader out of the targeting window, but you want to go with the low hanging fruit anyway. not the guy with shields.

The answer is once, because I don't put ordanance in positions to fail.  I put it one pilots with abilities geared to it, hedge my bets with a Gunner, or upgrades such as Push the Limit.

The OP is asking for opinions on his intial two Y-Wing two A-wing build.  This is not a thread discussing the merit of missiles or how to build the best squad ever.  He gave a general template to work in and that what we are attempting to do.  We are not talking about making missiles work we are talking about how to make his squad template functional.