see, i'm in the opinion that missile boats should be less effective and should only be effective when backed by a well organized team, ie, tag'ing and narc'ing. If a target isn't tagged or narc'd, then it should be much harder for a boat to be effective. The reason i think they shouldn't be effective is because it's super easy to use. Something so easy to use shouldn't be so effective. They sit still, make a circle turn red, then click a mouse button.

I know the Long Tom is supposed to be super awesome vs boaters, because boaters just sit there and fire and fire and fire.... the problem is,
the long tom is a new favorite of boaters to use. Long Toms just sit in the back, lobbing shells, except now, we dont even get a missile lock, we just lose 80% of our health unexpectedly. So imho, Long Tom is just another boat.
VTOLs and Aeros, yeah, they can be useful vs boats, but there are none on marshes, and the maps that they are on, they're easy to shoot down anyway (still scat priming the hell out of anything in the air). And yeah, with the increased AA efficiency, VTOLs and Aeros have an even harder time now.
Really what I'd like to see is the actual process of getting a lock with no team aid (tag or narc) being much harder. The problem is, it's inherently easy. We've discussed in past threads the possibility of increasing the time it takes to lock, giving an alert tone when someone has a yellow lock on you, then a different tone when someone has a hard lock on you, gosh... cant remember everything... dont allow LRMs to detonate within X seconds of being launched (no more tipping the head down to spam LRMs at someone right next to you)....
my personal favorite idea is a chaff/flare dispenser. It'd be manually actuated, and have limited supplies, but would guide away 100% of missiles if timed right. That would keep it from being too easy to use (fire them off too soon and the missiles would be able to discern between the distraction and the mech), and too late, well, the missiles would be past the distraction already so they'd hit you. Limited supplies means you still need to use your terrain to conserve your supply, so the LRM boat would still have a chance at you when you run out.
The C/F countermeasure system would not only distract missiles locked on you, but can be launched to distract missiles guided on a nearby friendly (within a certain range).