Why should maneuver get a bonus. Missiles don't get free fuel, free armor, sensors, or warhead. Why then free agility?
They do, actually get free engine efficiency. To elaborate, a 1.00 multiplier on engine efficiency at MSP 5, the max missile engine size, and one fourth the size of the smallest engine drive, while also requiring no crew onboard.
And I also figure that the built-in maneuver rating DOES have some rationale. Specifically, the idea that missiles are fully-designed to intercept a target, whereas ships aren't, then missile would simply be ten times better than ships at doing so, at the least.
That, and I think you're overthinking the base maneuver rating as something "earned" or a "resource", rather than just "base chance for missile-like object to hit, without agility tonnage devoted beyond 'be a missile'".
I mean if missiles got a free sensor included, and this scaled with the missile size, then there'd be something to counter the bonus that AMMs get from all that maneuver. But there isn't.
A sensor being added just for it being a missile seems superfluous. There's already a reason to design really big missiles with sensor space heavily devoted; they're called buoys.
The argument "why don't they get free (other thing?)" should be looked over carefully, because the answer will likely be "because they'd change the function of the missile where it otherwise should've been optional".
And as it's been stated that tere are no plans to tweak the armor system to make larger missiles more practical. There must be SOMETHING to make it worthwhile to load a missile larger than size 6.
Shock Damage? Long Range missiles? Long Range MIRV-style short-range-missile carrier stage? Armor penetration? Mines? Sensor buoys?