A few notes on Vanilla balance from my new exploration playthrough, which is a non-combat tree run.
1) Apogee is in a good place. It is a good exploration ship, but slow, and it is an acceptable hybrid combat ship. Its deployment cost is mostly right: it has similar battlefield impact to a Falcon because, like a Falcon, it has low DPS, but it lacks the speed and maneuverability to get out of bad situtations. Its strong shield makes it an acceptable anchor and the large missile slot can mount a Locust. It is very much inferior to Eagles and Dominators, but that is reflected in the deployment cost
2) Shrike needs a mobility system that can let it back up, for the AI if nothing else. Its absolutely find offensively and flux wise as a cheap light destroyer/frigate hunter, but the AI keeps backing off, then charging in again to get popped by proper combat destroyers.
3) Playing without combat skills is much more difficult. My fleet is about half as effective, maybe even less, than in my combat playthroughs. A fleet of Apogee, 2 shrikes (1 regular, 1 P), 2 condors, 3 shepherds, and a wolf are struggling against foes that I would comfortably farm with 1 Hammerhead, 2 wolves, 1 condor, because my personal ship is so much less powerful.
1) Apogee is a much stronger ship once it gets plasma cannons and Locusts. Plasma cannon is a bit rare, but Locusts have become fairly common now that pirates have the Atlas 2 (they sell what they use). Apogee is mostly fine, except maybe DP cost. 18 DP is too low if Paragon is any indication. (I think Paragon at 60 DP is too much unless it uses a specific loadout that uses Tachyon Lances.) With plasma cannon and locusts, Apogee is probably worth 20 or even 22 DP. But with inferior weapons, 18 DP seems about right.
2) I agree with this, but mainly for Odyssey's sake since it has the same system as Shrike, and AI is just as dumb with it on Odyssey. At least Shrike is cheap and disposable. Odyssey is expensive and a bigger problem. Despite Odyssey's flaws, player can make it work if he pilots it. AI cannot. It treats Odyssey much like on Onslaught and will burn head on into combat for a direct frontal assault, where it will get popped quickly by enemy capital or a mob of small ships because Odyssey has weaker defenses and firepower (without plasma cannons) than a proper battleship.
3) What would you call full combat build?
Generally, I go for Electronic Warfare 1, Loadout Design 3, Fleet Logistics 3, Coordinated Maneuvers 1, Combat Endurance 1, Evasive Action 1, and Helmsmanship 2 first, then get Defensive Systems 2 or 3, Gunnery Implants 3, and Power Grid Modulation 2. There, I get into decision paralysis because there are a bunch of other things I want but will not get enough skill points for them all. Among them, Ordnance Expert, Damage Control, Fighter Doctrine, Planetary Operations, Navigation, Colony Management, and Industrial Planning - all maxed. Plus Officer Management 1 or 2.
With industry limits and harsher demand for ores and volatiles, the Industry colony skills are not negotiable if I do not plan to depend on cores for my primary colonies. Even Planetary Operations looks very attractive for increased defense and stability. (Once Free Port in on, stability is too swingy with pirate activity and enemies stealing relays, nevermind stuff like Decivilized on the occasional planet that would be good to colonize.)
I agree with others that survivability is more important than mobility and offense for AI ships. (I do not put Helmsmanship on the few officers I have.) They do need some offense to hurt the enemy, but the ability to survive mistakes or to prevent mistakes that would plague weaker ships is more important.
P.S. Before 0.9.1a, I would have shrugged off Navigation because of the skill point crunch. It is convenient, but I was not aggravated enough to take it. Lately, after constant babysitting and big systems to slog through, plus fleet cap making four tugs hard to bring, I am starting to rate Navigation as high as max colony skills and will take it eventually, once I need to babysit core worlds much. Also, I do not remember pop-up bases spawning in neutron stars before 0.9.1, and dodging pulsar beams to kill a base and leave is a pain.