SpaceCat
I guess I don't understand why it needs to be possible to 100% counter missiles. No other weapon in the game can be 100% countered - even electrobolts will eat through armor given time. On stable I agree missiles need a very solid counter because they're incredibly deadly. On RC they deal very low damage, and take just as long (if not longer) to kill things as cannons, or lasers, or ion beams.
I get that missiles have unique advantages (long range and indirect fire), but so do all the other weapons. Lasers are pinpoint accurate and compartmentalize easily. EB shred shields. Ions are long range hitscan with the highest dps per surface area in the game. Cannons have penetration and start fires. If cannons, ions, EB, and lasers are balanced without a 100% counter, why do missiles need one?
Regarding hard counter rock-paper-scissors, I think that that's bad design for any game. While paper should definitely be favored against rock, a skilled/well-designed rock should still have a chance to fight back against paper. Look at Overwatch as an example (a game I play a lot). The hero reaper is a tank buster, and the hero winston is a tank. But a skilled winston can still outplay and kill a reaper - this keeps the game feeling fresh and reliant on individual performance rather than pure hero selection.
A Cosmoteer analogy: Should a wall with clustered reactors and horrible design be able to defeat a well-compartmentalized broadsider with an expert pilot? Walls counter broadsiders, but I think we all agree that design quality could beat ship type in this situation - rock could beat paper.
I think the issue is that we still view missiles as deadly ship-killers like they have been in the past. But now on RC, missiles deal less damage than cannons against armor, shields, and internals. Indirect fire is a nice advantage, but is it big enough that they need a 100% counter?
Atarlost
I understand your point about needing to win with minimal damage in PVE, but I don't understand why current balance makes that worse? Missiles on RC are strictly worse than cannons against both armor and shields (and internals). If missiles deal enough damage that you can't be cost effective, cannons or lasers or ion beams would deal far more.
Regarding shields and splash damage - I don't think splash through shields should go away entirely. Deciding how close or how far to put your shields has always been one of the fun parts about shield placement, and removing splash through shields would take that away. But, I do think that right now closely-placed shields "feel" ineffective because psychologically it seems like they're not doing anything. If you test it out though, the closest shield possible still reduces missile damage by roughly 1/3. Medium or far placed shields reduce missile damage by much, much more.
Mc2
I agree, and I think that this is backwards from the way it should work. Missiles are incredibly surface-area efficient, so PD should be surface-area efficient as well to counter them. Surface-area efficiency and protection area should be what sets PD apart from shields and armor, not cost-efficiency.