I didn't vote in the poll, because I've found a combination of several of the options you've listed works relatively well.
a. Reducing chopper range - not only does it make sense realistically (choppers are fuel-hungry, low-range units compared to jets), but it reduces their attack capabilities to 2 or 3 per turn at the most
b. Increasing air drop penalty - hard to argue against
c. Increased prototyping costs - again, makes sense (air units are far more technologically complex than ground units) and double cost for prototypes is not prohibitive
d. Cost of drop ability rises with weapon and speed - that's a great idea I hadn't considered before
e. Increasing intrinsic base defense - I think bases are absurdly easy to take in SMAC under the default settings; realistically, unless an attacker has a tremendous technological advantage, he should be suffering twice as many casualties as the defender as he takes a base. This is the #1 factor contributing to chop & drop - being able to sweep through base after base without losing a significant attacking strength
I think players don't plan their defenses well enough to repel attacks from combined forces. It's common practice to design one type of base defender, when there should be anti-air (AAA SAM) and anti-ground (comm jammer / trance) units in combination. Hence, I tend to think that strengthening defenses and re-thinking defensive strategies are more appropriate than weakening the attack abilities of air units.
That's my $.02