I tend not to play with any player skills nowadays for the "pure" experience. Which is basically false purity anyways, because many fleet skills are bonuses to player piloted ships anyways.
Ohase ships are good even without missiles. For instance an Afflictor with 2 Antimatter blasters and 2 Light Assault Gun is similar enough to reaper afflictor but with more staying power. Likewise with Shade. They can all point their guns forwards. Though it can be argued that in this case it is AM blaster that which makes it similar in style. Shade is almost an Afflictor. It's supposedly a little weaker, but EMP Emittor ship system is simply brilliant. Who needs Ion Cannons when you have EMP Emitter.
Personally I like to see Afflictor or Shade variants not as phase ships but as normal ships with shields, but I suppose we don't really need yet another specialist rare frigate to chase down other normal frigates.
I tend to stay away from a lot of skills simply because they make the game too easy and don't change the gameplay enough. Which is really my biggest issue with the current skills as they are: Instead of increasing my gameplay options, the skills are largely just "Vorpal Sword +3" buffs.
Skills I like:
Navigation 3 because it gives you transverse jump
Sensors 1 because it gives you neutrino sensors
Safety Procedures 2 because it makes fighting in alternative terrain like the corona of a star more viable
Skills I don't like:
Salvaging - Just trivializes the loot mechanics and prints money for you
Combat skills - Virtually all of them, as they just make your piloted ship overpowered (the exception for me being combat endurance)
Loadout Design - Like the combat skills, it's just large buffs that unbalance a lot of ships which are fine otherwise
Combat endurance is quintessentially the skill/buff I think officers should be applying to ships - they can fight longer with fewer malfunctions and get minor bonuses to a few stats when the CR is at a high level. I think that works a lot better for balance and makes more sense with "elite" ships run by an actual officer.