I always micromanage titans. Cap ships I will also initially micromanage but as my Empire expands I may turn auto cast on some of the more reliable abilities like the Dunov's abilities (except magnetize), the Skirantra's scramble bombers etc. 

The Celio command cruiser's designate target is the only one for TEC, I usually have a pair late game just to manually use that ability on key targets. Repulse is perhaps the scariest ability in the game when manually used by a good Advent player. And of course microing a large number of overseers can make nearly any ship immortal, and Subverters should always be microed so they don't just disable a single ship.

people say.. Repulse of your own or try to snipe those things out with strike craft (good luck with that, low efficiency of SC damage type against these..).

Nerf? It's multiplayer only, in singleplayer that ability is totally useless (for me it seems this way, I only used this once and did not find it to be useful), I don't think it will ever be changed unless everyone starts crying this is OP (but considering Advent still have many weaknesses.. I don't know). And the majority of players are from the SP group.

Better to use it when the fleeing ship is 2-3 seconds before initiating phase sequence (so almost facing the right direction), hit it with ion bolt, meanwhile focus fire with everything, hit it with another ion bolt when the cooldown is over and his ship is in the middle of opening the phase window, almost guaranteed loss of enemy capital ship (assuming you have the necessary firepower there). Ion Bolt alone is not enough to stop a ship from jumping, the cooldown is just too slow, you need to use it carefully to have higher chance of success and not having to chase the escaping capital ship having 100-200 hull points left..

Repulse DOES affect titans. Thats one of the reasons why its so dangerous.