As cherse stated in his topic in the Questions forum, strategies only affect default unit categories. This makes things a little ridiculous in scenarios where the only default units are, say, infs and militia, and the only strategy that makes sense is PD. If strategies affected custom units more, the difference between strats would be more noticeable, especially in maps that add many more naval units, air units, commanders, or ground transports. Below are my suggestions for how strategies should affect units.
But before I jump in, I also think there should be a check box that asks whether you want a unit to be affected by strats. For example, in EC's Ancient World (and a few other maps) there is an incredibly expensive immovable wall you can build. However, when you use Blitzkrieg, you can actually walk the wall around which is completely illogical. This is the sort of unit you don't want to be affected by strats.
Great Combinator:
Ground Secondary Attack: +1 attack, -3 defence
Ground Special Attack: +1 attack, -3 defence
Guerrilla Warfare:
Ground Transport: +150 cost, -2 range
Ground Secondary Attack: -2 attack, -2 defence, -1 range
Ground Special Attack: -2 attack, -2 defence, -1 range
Iron Fist:
Ground Transport: -2 range
Master of Stealth:
Ground Secondary Attack: -1 attack, -1 defence, -1 range
Ground Special Attack: -1 attack, -1 defence, -1 range
Naval Commander:
Naval Secondary Attack: -20 cost, +1 attack, +1 range
Naval Main Defence: -20 cost, +1 defence, +3 range
Naval Support: -50 cost, +10 view
Naval Special Attack: -20 cost, +1 attack, +3 range
Naval Commander: -100 cost, +3 range
Naval Other: -20 cost, +2 range
Ground Secondary Attack: -1 attack, -1 defence, -1 range
Ground Special Attack: -1 attack, -1 defence, -1 range
Perfect Defence:
Ground Main Defence: +1 defence against Ground Secondary Attack
Ground Secondary Attack: -1 attack
Ground Special Attack: -1 attack
Ground Other: -1 attack
Naval Secondary Attack: -1 attack, -2 range
Naval Special Attack: -1 attack, -1 range
Air Secondary Attack: -1 attack, -3 range
Air Special Attack: -1 attack, -2 range
Ground Commander: -100 cost, +1 range
Tank General Relentless Attack:
Ground Secondary Attack: -10 cost, +1 attack, +1 defence, +1 range
Ground Special Attack: -10 cost, +1 attack, +1 range
Ground Commander: -100 cost, +1 range
Sky Menace:
Air Secondary Attack: -10 cost, +1 attack, -1 defence, +1 range
Air Defence: -20 cost, +2 range
Air Other: -10 cost, +2 range
Air Commander: -100 cost, +2 range
Ground Secondary Attack: +10 cost, -1 attack, -1 defence, -1 range
Ground Special Attack: +10 cost, -1 attack, -1 defence, -1 range
Post suggestions below and I'll edit into the list.