I can see setting up a "doctrine" technology tree for VBAM. In the real world it wasn't just a matter of the sophistication of the equipment used in combat, but the actual skill of the troops that used the equipment.
WWII example (I'm going with ground combat here because I've been playing West End Game's "Front" series with my brother recently). Germany had inferior tanks to the Soviet Union when it invaded in 1941, but the Germany tactical skill made up for this and allowed them to defeat the superior Russian tanks (in both quality of armor and armament and quantity of tanks on battlefield) time and time again. Using combined arms techniques the Germans were able to maximize the effectiveness of their available units in any given battle.
VBAM doctrine technology could start with the 4.3 Advanced Dedicated Mission rules from the CM book (pg 73-76). Just because you have units with long and short range capability if you don't have the tactical doctrine in place to capitalize on these abilities, you'll not reap the benefits.
A second layer of doctrine technology becomes available as well based on actual combat experience. After a class of ships has seen combat (doesn't matter who won the battle, truly professional military learn as much or more from defeat than victory), they will have chance to develop specific doctrine (tech) to further enhance their ablities.
Escort class ships would be able to research "Squadron Screening" and earn a +1 DV once completed or "Squadron AF tactics" to gain +1 AF. Scouts would have to research a specific mission type (squadron defense would be the default role scouts could do) which would make them less "overpowering" unless an empire dedicated serious EP for maximizing them with all available missions.
Command ratings and command cost could also be affected by this, with destroyers going from CC 2 to CC 1 with "Precision escort squadron formation flying" (which is a CC -1 tactical doctrine). See below for class breakdowns and restriction suggestions.
I'd break down VBAM ships as follows for tactical doctrine research purposes:
Escorts--corvettes, destroyers, frigates, etc
Cruisers--light, heavy, attack, explorer ships perhaps
Carriers--anything with carrier special ability
Capital Ships--battle cruisers and so forth
Scouts--the EW boys
Attack Boats--and maybe heavy fighters here too since this is "gray" area
Fighters--I wouldn't break them down by size (light, medium) but maybe by specific type: AS emphasis, AF emphasis, "balanced" fighters (AS 2, AF 2 for example) would be "multi-role" fighters and able to research both AS and AF doctrine trees.
And just like the 10.0 Elite Officer and Crew rules (CM pg 201), no ship, fighter, etc can gain more than double (or half) its original value. So a frigate with DV 3, AS 1, AF 2 can only be increased to DV 6 even if empire has "Squadron Screening +4". And the DD going from CC 2 to CC 1 would not be able to go to CC 1/2 (since 1/2 is below half the original class CC of 2).
That is my "organized" initial thoughts on the topic that I've wanted to propose for a while so I hope that gets the ball rolling in a constructive, helpful direction.
-Mark