Right now there are major disparities in the strength of the three captain types and their abilities in space both in PvE and PvP.
Tactical: The abilities of the tac captain are the most universally useful and effective as they primarily boost the damage capabilities of any ship they fly and allow for expanded roles when piloting cruisers and science vessels beyond what the ships themselves normally possess. They are pretty solid aside from a few tweaks to keep them from overshadowing the other types.
Science: These abilities are fairly solid and while they do not expand the roles of escorts or cruisers by a large amount they are still effective when piloting them. They mostly could use some tweaks and minor boosts.
Engineering: The worst of the bunch. The abilities that increase their durability are mostly unnecessary and not very effective and the damage and utility abilities are fairly weak and limited in effectiveness.
Science Ability Specifics Sub Nucleonic Beam: An extremely powerful ability in PvP but limited in effectiveness in the majority of PvE encounters. To help offset this I would allow it to place a minor debuff of a target's Sensors skill.
Sensor Scan: The second best PvP and top PvE skill it is extremely effective. But in order to secure a science captain?s dominance in energy drains and crowd control I would add an additional debuff to a target's Flow Capacitor and Inertial Dampener skills. Slightly reduce the resistance debuff or remove the stealth debuff if necessary.
Scattering Field: Solid ability but perhaps it should also increase Inertial Dampener and Power Insulator skills as well.
Tactical Ability Specifics Attack Pattern Alpha: This ability is extremely potent at increasing a players damage potential not just because of how it multiplies all damage but also increases critical damage and chance for an additional multiplier. Because of the fact that it effects criticals, and that tactical captains do deal an inane amount of burst damage with science abilities that can no longer crit I do not feel it should effect boff abilities in any way such as Gravity Well, Photonic Shockwave, Directed Energy Modulation, etc, allowing the abilities themselves to be buffed a tad. The remaining Tactical captain abilities still should boost those damages though as a sort of compromise.
Go Down Fighting: Is simply a very weak attack pattern alpha with a longer cooldown and lower bonuses. Perhaps adding a small hull resistance bonus that increases like the damage bonus starting at say 20 would really help give this ability a niche role.
Fire on Mark: Really good ability in PvE but semi worthless in PvP thanks to tac team. Perhaps a secondary effect of reducing an enemies defense bonus that was cleared by engineering team and slightly reducing the primary effect would be a good change for all.
Engineering Ability Specifics Rotate Shield Frequency: While it is a solid ability it is not that useful. Allow it to be used on another player and for both the target ship and the caster ship to gain it's effects.
Miracle Worker: Does not live up to the name because it simply heals once without any buff attached makes it less effective at keeping you alive than a simple Epower to shield would. First, allow it to be used on other players. Second, increase the hull heal. Third, allow it to clear ALL debuffs. Lastly it should grant a shield and hull resistance bonus for 10-30 seconds of around 20-30%. Then it would be worthy of such a name and allow even an engineer in an escort to save someone's day.
EPS Power Transfer: While great in theory it is already so easy to run at nearly full power it is only remotely useful as a minor DPS boost in a beam boat or to save you 200 EC on a battery. Instead allow it to increase the effectiveness of all power levels by 30%. So if your weapon power level was giving you a 100% damage increase now it gives 130% and so on. Or alternately allow it to increase the hard/soft cap of power levels.
Nadion Inversion: Good in a beam boat nearly worthless with cannons. Add a flat damage bonus to hull like directed energy modulation to the ability and your good to go.
While it is true that I am advocating a minor nerf to tacs I do not think it would be unreasonable. In addition I do believe that these proposed changes would allow the various captains to bring more to the table when piloting both their standard ship type like a tac in an escort, and to bring a unique role to the other ships like an eng in a sci vessel beam boat that can deal some DPS and buff/cleanse/heal like a boss, or a sci in an escort that brings great team support.
APA, GDF, and Tactical Fleet should all remain 100% potent when used with powers that deal damage. Period.
Do not underestimate Go Down Fighting. It is an, up to, 100% increase in net damage. Sort of the ultimate Attack Pattern. It runs a solid minute and its practical damage boost is based entirely off of your health when it is activated, not what your health is at any given time during it being up.
You also neglected to compare Fleet Skills which are very powerful group buffs that are (at least for Science and Tactical) to be underestimated. Tactical Fleet is a team-wide 30% increase in out-going damage. Science Fleet is a team-wide Shield Regeneration and Resistance Buff.
Regarding Sensor Scan, did you mean debuffing their Power Insulators and Intertial Dampners skills? Oh, and a sensor system penalty isn't going to make Sensor Scan any better in PvE in any appreciable way.
Don't forget to note that Scattering Field is an AoE that affects yourself and nearby allies that pass in and out of it.
Pointedly, the non-Engie Captain powers are pretty much top-flight across the board. FOMM is weak because in PvP Tactical Team is everywhere due to its must-have shield auto-balancer.
Miracle Worker as a targeted Panacea skill I could get behind. Clears *all* non-tactical debuffs, hits the target with a flash hull and shield heal for about 12k/4k respectively with 15 sec of 35% resistance both ways.
RSF as a self/or target ability, with Miracle Worker, really would make the Engineer the healer to beat.
I kinda like your idea for EPS Power Transfer.
Nadion Inversion isn't even supposed to suppress weapon drain under the current system, it is, last I heard from the devs, a bug. No real complaints with your suggestion.
Oh, well, there is one small problem with jacking up the team healing capability of the Engineer... you're going to need to nerf every other healing power in the game.