Add large I+D facilities similar to actual factories, and if NOT destroyed, perk rides would lower their cost along the time. Damage to these facilities would have the opposite effect, increasing the perk cost.
For example, start any tour with actual perk base doubled and if these strat targets are undamaged (supposedly well deffended) for 1 hour, perk base per plane is halved (perk plus per population remains the same). Undamaged factories for 4 or 5 hours may enable some special weapons or planes, and may lower the perk cost to 0 (except any plus due population). Damaging these facilities would increase perk cost and, if totally destroyed, perk rides and special weapons would be disabled at any field.
Make these facilities "secret", so a map can have them located in several optional places. The location of these facilities would be determined once a new map is loaded, choosing ramdonly between the optional possitions. And dont show enemy I+D icons in the clipboard map until these facilities are located (having a friendly plane closer to 10 miles from them).
Ar234 may be a good choice to perform fast attacks against these facilities (once located).