In your current assignment, NATO wants Serb behavior changed. NATO can apply military pressure to achieve the change, or not. If NATO decides to apply it, it needs to select the form and degree of it. Serbia then can decide to respond, or not. If NATO selects bombing from the air, Serbia can respond with its ground-based defenses, or not. It can also decide to respond with its air force, or not. If Serbia chooses to respond with its air force, it needs to select a means and a degree. One choice is to harass the NATO bombing aircraft when near their ground targets, and another is whether to press attacks by aircraft on NATO aircraft to shootdown, or not. If not, the choice might only be harassment so as to preserve Serbian aircraft to fight/harass other days. (A campaign perspective helps to make this choice.) If Serbia chooses to respond with its air force by harassing NATO aircraft (only), NATO needs to choose how to respond. One possible choice is not to respond — and simply accept such punishment as a small/backward air force can exact. (NATO aircraft carry a small number of AIMs without sacrifice of any air-to-ground attachment points on its aircraft.) So NATO could alternatively respond by using only those AIMs.) Or NATO could go further by using some of its attachment points for AIMs instead of air-to-ground ordnance.   When the bombing campaign starts, NATO has the potential to fill all its aircraft attachment points not specifically designated for AIMs with air-to-surface ordnance. Or NATO could give over some attachment points to AIMs. Or, for some aircraft in the squadron you are advising, it could give all of them to AIMs for some of the aircraft in the squadron.  

The role for analysis in all this is to sense what the (adaptive) campaign goal is and assess performance in achieving it by observing performance at it. With luck, usable data insights on performance will be available to the analyst.   Since, in advising your squadron, you don’t yet have data on its performance, your advice amounts to sifting operational objectives to fashion a policy. Whatever your advice, you might modify it later based on data about the policy that would follow…

Additional questions to help answer critique:

There is a difference between an observation and an assumption.  For example, Stillion observed that USAF pilots fall into 2 groups in terms of their bombing skills.  It’s an observation, not an assumption.

Regarding your 3d assignment as analysts:

-The problem assigned is more one of sifting operational objectives than of seeing what difference higher technology makes to squadron performance.

-If the squadron were going up against an opponent of comparable skill, husbanding air-air missiles would be a primary consideration because firing most/all you carry could yield a disastrous outcome if the enemy turned back for more dogfighting.  But if the opponent is disinclined to fight head-on, being freer with AIM usage is more permissible since the enemy rarely shows up and doesn’t stick when showing.

-The $ cost of AIMs isn’t a major concern.  The marginal cost for firing an extra missile is small compared to the total cost of the bombing-campaign operation.

-Your squadron’s aircraft (12-15 per squadron) don’t all fly on the same mission.  Those that do are multi-role-capable.  That is, any aircraft can carry all air-to-air ordnance, all air-to-surface ordnance, or mixtures.

-The inflexible time-over-targets displayed in Vietnam wouldn’t be matched today.  Night-capable flying by NATO frees up the flying schedule, and Serbia would take advantage of fixed times as North Vietnam did.

1. NATO is aiming to push Serbia back so are the targets primarily Serbian military routes and installations (but not their Air force base?) YES
2. Are we recommending how many of the planes in the squadron should have surface to surface and air to air to both complete their mission objective and eliminate serbian forces that aim to harass NATO forces?  THE MAIN GOAL OF THE CAMPAIGN IS TAKING OUT GROUND TARGETS.  AIR-AIR COMBAT IS A DIVERSION FROM THAT.  BUT YOU CAN’T KNOW WHEN SETTING OUT FROM BASE WHETHER THE SERB AF WILL RISE TO CHALLENGE.  HOW MUCH OF YOUR AIR-TO-GROUND WEAPONS LOAD DO YOU DIVERT TO AIR-AIR, AND HOW DO YOU USE IT WHEN SERBS DO RISE?
3. In the recommendation are we prescribing time of day to increase effectiveness of the attack? IF YOU WANT, BUT IT’S NOT CRITICAL
4. NATO’s goals are to move the Serbian troops back, does it fall on us as the analysts to set what the targets are and thus that determines what weapons the planes carry? NO, YOUR ISSUE HERE IS DIVERSION FROM FULL WEAPON LOADING FOR AIR-TO-GROUND