Are we talking Sins or Entrenchment? Which versions?
In Entrenchment it is still next to useless to leave stuff on auto cast. Almost all skills as Vasari can not be trusted to be auto cast even in single player.
While you may think that this is fine because a certain amount of micro should make a good player we have to remember that the AI uses this auto cast so the AI is as stupid as these auto cast decisions. It would be nice to see the AI not crippled by this stupid ability usage.
Some examples where there is obviously not enough conditional checks where skills are just wasted:
Kortul Devastator
-Power Surge = Fine to auto cast
-Jam Weapons = I can't really tell, I don't watch this much
-Volatile Nanites = You would have to be mental to auto cast this, a Kortul will happily target the single cap it wants to attack rather than the group on the other side of him that includes another cap. It prioritises whatever it would normally prioritise as it's main target and that is more often than not not what you would want.
Skirantra Carrier
-Repair Cloud = fine to auto cast from what I can tell if you aren't worried about efficiency (it will cast if one ship need 10 hull)
-Scramble Bombers = auto cast = 0 AM but I believe that's an issue with the skills usefullness rather than the auto cast behaviour
-Replicate Forces = No way. I tried it once and my Skirantra duplicated some carriers. You would think great right? It wasn't till I clicked on them I noticed the duplicated carriers didn't have any strike craft set to make....
Jarrasul Evacuator
-Colonize = Mostly ok, I manually set this off when I really don't want it to do it.
-Gravity Warheard = God no, it spams it on it's target, it doesn't consider whether it is fleeing or not, why waste AM on a target that is standing there shooting back?
-Nano-Disassembler = Haha no way! Same as Volatile Nanites it just shoots it when it's off cool down at whatever it is targeting. A LRF with 62 hull and no shields left? Yep that's fine for auto cast.
-Drain Planet = No problems there really, not seen it do it in combat
Antorak Marauder
-Phase Out Hull = Auto Cast is detrimental to your own fleet, rather than locking down a single cap it will hit a cap, then as soon as CD is up use on another ship as the original isn't phased back in yet. The net effect is your fleet is forever changing targets as the current target is phased out. Just takes longer for you to kill stuff, useless.
-Distort Gravity = I leave this as auto cast, it's fine mostly, only falls apart when your Marauder is targeting something that is away from what the rest of the fleet is targeting, no big deal.
-Subversion = Don't know why you would want to auto cast this so who cares anyway?
-Stabilize Phase Space = Same as subversion
Vulkoras Desolator = I am forever microing auto on and off on my Desolators
-Phase Missile Swarm = Generally fine just have to micro this if I need AM for Disintigration.
-Deploy Siege Platform = Pretty useless to auto cast this, the Desolator does it in combat, often flying far away from combat to cast then fly back. Maybe you want that sometimes but in 90% of cases I would prefer my Desolator to only auto cast this if it is not engaged in combat.
-Disintegration = The auto cast is useless, it's as stupid as Nano-Disassembler and I've not noticed if it only uses it when it needs hull? Personally I save this for SBs so I don't auto cast it until it's time to clear one of them.