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The '50% of missiles delete themselves' thing turned out to be the half damage from being out of energy hitting the guy who was doing the tests. There was a version of that thread on these forums where that eventually came out.

Oooh thanks for the info! The thread was never updated (or ever caught wind) on the stellaris subreddit. I only come to the PDX forums and reddit in between classes, so I'm not surprised I missed it. I'll rule out most of that thread for now then, but I do have some personal experience trying to balance missiles and PD. I even tried balancing around having no PD except flak once, but that made very little sense (although it partially worked).

Focusfire and Overkill.
Random fire and underkill.
You use one, you get the other. Holds true as far back as Age of Empires:

The problem is that Regeneration (shields and HP) might apply ,so random firing would upgrade the side with regeneration massively.

Well the extra issue is that micro isn't something you can do in stellaris, only the "AI" can. When a human is in full control of the army, micro heavy battles can be absolutely insane, even from Starcraft 1 which was only a year after AoE1. If you want examples from SC2 (easier to read) for how micro intensive players can get, check these WCS highlights. Nerchio and Showtime are sitting pretty at 300-600apm (5 to 10 actions per second) during the climax which is out-of-this-world fast.
For AI it has to find some level of middle-ground where it can say "this is how fast I should go". For grandmaster players of SC1 and SC2 overkill and underkill are rarely a problem, but that's running off of brainpower and not an AI working off your computer's resources. If we're to look at how many APM each fleet is allowed to have and overall is capped at across all fleets, we have to cut it short to save resources for the rest of the game otherwise we run into moments where the game will be too resource intensive to accomplish anything other than dropping your framerate to 1. There are so many facets to this (particularly with missiles) that it really does take insight from the people programming the AI at PDX in order to move forward. Quite unfortunate but we simply lack the insight they have. This doesn't mean we should drop the topic, of course!
 
Fought against a species that had Missiles, and anything that didn't have PD died........ but the 8 destroyers that had PD survived and killed everything else.

Just seems as though in the early game, Missiles are really good against those who aren't prepared for it.
 
So whats status of missiles now after the buffs?
Less bad, but still not player usefull. To quote Wiz:
It's a stopgap measure to give them some utility while we fix the more fundamental issues like retargeting and how PD works.