A term I've encountered in another online game (used by its designers) is "anti-fun". In short, something is anti-fun whenever it causes more grief on the receiving end than it is fun for the one using it. I firmly believe most covert ops and SKs fall into this category.
To 'fix' covops there need to be rewards. Most of the time, taking Science Hack as an example, you just pick a target at random and hack it. Very rarely do you consciously pick someone so that it actually
benefits you. You pick it just to cause grief. What could make it work better is basing the amount lost on the target's output and giving you (a part of) that output. For example, with 10 agents you
steal 10% of their Research output for the next 4-6 ticks (this also fixes the ridiculous amount of research you can set back if he's researching a 7200RP research rather than a 1600 one). If you get Science hacked again before the duration is over, the reduction doesn't stack but is applied anew.
Other Covert Operations:
Code:
Network Charting - Rather unsure about this. Perhaps it could steal stealth (from planets with higher than 50 Stealth), so you can recover after a previous one?
Exploding Fist - Another one that's of limited use. Stealing asteroids could work but it'd be funny to see a secret agent with an asteroid on his back on the subway...
Sabotage - This one's fine, it has its uses and doesn't cause much rage. It even has counterplay for the target.
Security Guard Poisoning - Again, fairly useless. Could be changed to incapacitate someone's entire staff of Guards for 2-4 ticks to set up for a new covert op. If you succeed on this one, of course.
Information Blackout - No comment, it has good uses.
Hacking : Resource Transfers - Needs to be less powerful early in the round and scale better. Suggest to be based off of income rather than stock.
Havoc - Remove this or make it targeted towards Factories.
SKs I have no direct solution for. Like Havoc it's hard to just let someone 'steal' Constructions. I just feel they cause way more grief than they're worth. You can kill a hundred ticks' worth of Constructions with too little effort or reward. Honestly I wouldn't mind seeing them removed, but I know a fair amount of people wouldn't agree with me on that front.
Feel free to make suggestions on how to improve them, though.
In conclusion, give Covert Ops rewards to make them actually beneficial, rather than some measly XP.