Just started playing again and I'd like to mention something that Alex probably forgot:
After all the recent changes, a lot of the "Missions" (IE: Standalone battle scenarios) probably need to be re-examined and re-tuned. With the new ship abilities, improved enemy AI, and balance changes to some weapons, some of the battles that were balanced before are now incredibly lopsided.
'For the Greater Lud' is one that really stands out. With the default setup, it's gone from a fairly straightforward scenario to a quite frustrating one. The enemies are always spot-on with the shielding now, and the default setup gives you NO weapons that are any good against shields. And with the improved ballistic weapons and better accuracy, the enemy fleet will quickly shred all of your bombers and sweep you off the map.
Mind you, I'm not saying it's impossible by any means. Just VERY difficult. Meanwhile, refitting a few of your ships with different weaponry makes the entire scenario easily beatable.
Several scenarios have this problem now. The main issues seem to be:
-The AI in general has gotten far better. This makes a lot of the scenarios where the player has to save the day due to superior skill much harder. They don't make many mistakes and leave few openings. While I'm happy it has good AI, there should probably be some sort of level adjustment for it (Based on crew rank/admiral rank, ect) so that rookie-crewed ships aren't shielding perfectly and landing every shot like Elite crews are.
-The High-Tech ships seem to absolutely dominate almost everything else. It was rough enough when they just had better shields and more maneuverability. But now they have things like teleportation, terminator drones, and phase-skipping. Most missions where you control the high-tech ships are significantly easier, while missions where you are against them can be incredibly frustrating.
-With the addition of the Burn Drive, a lot of scenarios get messy on such small maps. ESPECIALLY the "Catch the retreating enemy" scenarios like 'The Wolfpack'. With the Burn Drive and the small map, they can clear the entire screen incredibly fast. Again, not saying it makes the mission impossible, but it inflates the difficulty a good bit.
TL;DR: The Missions need to be brought back up to speed after all the changes to the game.