I'll break it down a bit.
First up:
Nothing's unstoppable if you can dodge it until you close to your own weapons range, and evasive action is in Total War. What are the odds of a gunnery 4 ship hitting you until standard long, if you're playing it smart by evading and turning for side aspect mods?
I have trouble taking this post as anything other than you declaring that the accuracy of Capital Missiles is too unreliable beyond Standard Long Range which matches up pretty close with Capital Medium. Thinking about it and thinking about the answer to your question there I admitted defeat in my argument of Capital Missiles being over powered.
But then I get this:
They're still nice for smacking fighters outside of their own weapons range.
Just because they're not unstoppable and just because a tiny handful(proportionate to the total population of military DropShips) can make themselves really hard to hit with them without resorting to odd maneuvers doesn't mean they're a terrible idea. Just means they're not the be-all end-all of large craft weaponry and, like everything else, you have to think about their deployment to get the best use out of them.
Why wouldn't Dropships and ASFs evade when you know Capital Missiles are in play, especially under the Total Warfare AMS rules?
Especially when as I pointed out ASFs are even better at evading?
So if by your first quote I made there the expectation is that Capital Missiles are too inaccurate under Total Warfare rules to hit beyond Capital Medium Range with what you can do via just Total Warfare then how is this statement of mine incorrect:
Capital Missiles are a terrible idea and should not be considered without significant optional rules to make them even remotely useful in any role.
Because when you do consider their sheer mass and cost other weapons in Total Warfare make much better sense to mount in their place under the rules found there.