Smaller craft like the space shuttle can be moved with thrusters faster and easier then a large ship, which creates a harder target to hit. Simple physics.
Trans-Newtonian drives are inertia-less, so large craft can jink just as well as small craft. Steve made a concious design decision to abstract away jinking by assuming that fast ships are better at jinking than slow ships, with an effect proportional to the speed ratio.
Fighters have a smaller cross section, making it harder to hit
For a moment, I thought this might be a winning argument (at least for beam fire), but then I realized that it would kill point-defense beams. The problem is that a 5HS fighter is ~16x larger than a size-6 missile. Even if you throw in a power of 2/3 to take area vs. volume into account, this means that anything you do to significantly reduce the odds of a weapon hitting a fighter will completely kill the odds for that weapon hitting a missile. The same argument applies for missiles.
If I recall Missile Do currently have an evasion/manuverability bonus, with the Agility score already, whereas a fighter does not have this bonus that I can see, or ability to modify this bonus, unlike missiles. The argument missile code would have to change is flawed as the code is already in for missiles.
As Brian said, this is an offensive bonus - defensive agility is considered to be already taken into account because of speed. Any change to this would probably imbalance in favor of missile agility.
On follow when it slows down the speed of the fighters is where the target enemy has the best ability to shoot down the fighter, whereas in reality it is the opposite close into the guns the fighters buzzing around are harder to hit with minimum windows of opportunity to target as it crosses the in and around the vessel.
Now this one I REALLY like, although if there were other ships besides the followed ship you'd have to consider follow mode to be "zero range", i.e. the distance between the fighter and the followed ship would need to be small compared to the radius of the followed ship, otherwise the escorts could simply shoot the fighter off. The problem here is that point-blank range is 10,000 km, which it takes a typical fighter a second or so to cross (forever in computer time). So the idea (it sounds like) is that the fighter closes to zero range, at which point the target ship's weapons can't bear and escorting ships' weapons can't fire for fear of misses hitting the target ship. The really fun part here would be to allow the escorts to fire at the fighter, but to have a probability of misses hitting the target ship, based on the target ship's size.
Another nice thing about this idea is that it doesn't affect missile balance - once missiles are at zero range, they'll simply attack, so they can't take advantage of it. And another one is that the benefit should be bigger for big target ships - it gives the "gnat-like fighters vs. lumbering behemoth" feel.
I also like (and hope Steve will) the aspect that it doesn't make fighters harder to hit while closing. So even though you're giving them a "safe zone" once they're up close, they'll probably still take heavy casualties on the way in.
Finally, the effect isn't a "fighters-only" thing - a destroyer could use it too against a super-dreadnaught. The important part is the size ratio and speed advantage between follower and followee.
As a sanity check, I wonder how this would change
Star Swarm Attacks.
John