Notes

This skill tree is used for many different builds as this is my main character on my account. This means that it could be optimized for just one or two builds, but servicing all main archetypes requires a few concessions in the "Advanced" skills in order to pick up some basic skills elsewhere. I'll go through each node and why I chose the amount I did, though sometimes it's simply "I ran out of points".

For Hull/Shield Restoration/Capacity, I like to pick up one point of each, however shields have really fallen out of favor. 50 points in each skill is quite a lot, and heals are needed on every build. With the current state of the game, shields are pretty meaningless. I do pick up the Regen later on, but of the base skills I don't feel they are necessary. If you really want some extra shields, pick up the Valdore and use it's console for some really large shield heals. 

For energy/projectile weapon training, there's no real reason to skimp on these points. All of my builds use torpedoes and/or mines, and several use many energy weapons as well. Having all 6 points is like having the Cat1 from another 1 2/3 Advanced Consoles for every weapon type.

EPS is another quintessential energy weapon damage skill. This combined with emergency power to weapons helps mitigate losses from firing energy weapons. Since several builds sport many energy weapons, this really helps those. This also helps recover from Full Impulse and Auxiliary to Battery much faster. This makes it a very useful utility skill for every build. Both points means I get 5 power every 0.5s rather than 5 power every 1s, essentially double the effect.

Full Impulse Shunt is a waste of a point in my opinion. While this keeps more power in systems while at full impulse, strategic flying can remove the need for this. Short bursts of full impulse doesn't allow for much power to be drained, and in cases where long distances need to be traveled, coming out of Full Impulse a second or two early can mitigate these issues (especially on such large ships as I fly, they power slide regardless!) If you run Miracle Worker Primary as many tanks do, this instantly restores power after coming out of Full Impulse making this point absolutely unneeded. 

Impulse Expertise is just about essential. None of my ships turn well and don't have a lot of power left for engines after putting it in Aux or Weapons. This helps me keep up with everyone who uses those Competitive engines, or actually turn around before the queue finishes. I could argue for an extra point to take all 3 here, but ended up needing the point elsewhere. The last point is only 4% anyways, so I am not missing much. 

Control Expertise (CtrlX) and Drain Expertise (DrainX) are skill points many leave off. I always spend one in each, not only for their offensive utility, but also the defensive benefits against controls and drains. In the case of my Tholian fleet, all three use the Web Cannon and Webspinner, which hold for a specific duration. That duration is increased by CtrlX, so I can't really get enough. Also, being hit by Gravity well or Tractor Beam reduces some damage resistance is fantastic for all 3 builds. Drain Infection is an odd choice, but as a DoT, it really serves as a trigger for other abilities when it hits.

Targeting Expertise is an iffy one for me. Parses show I never miss, but they don't show how much extra gets turned into criticals. I feel like the first two points can be justified, but the last point is a pretty small contribution. I may even drop the third point in the future, but we'll see how the resulting accuracy shakes out. Defensive Maneuvering is also tough because of how much actually moving factors into the equation. For now, I feel like I can justify two points, especially since this is harder to come by than Damage Resistance Rating.

Hull Plating is what I would spend the extra Defensive Maneuvering point in, but this isn't all damage resistance, but pretty close. Some of the more exotic sources such as Fire and Radiation aren't present. Also, all this is only 15 actual damage resistance. All 3 skill points in the Hull Plating is equivalent to the damage resistance of Repair Crews.

Damage Control is awful, it's 1/5 as effective in combat. That means one point is 10% regen, whereas 2 1/2 points in the Hull Regeneration endeavor is that amount.

Shield Regeneration is special for some special reason and is extra effective. I always put in at least one point here.

Shield Hardness is something that mitigates damage while your shields are up. However, I tend to go for more Hull than Shield defenses. My tank (totally different character) often will have absolutely no shields in deep combat and relies on Regeneration and large capacity. Reverse Shield Polarity is still really strong, but Shield Hardness doesn't really boost that.

Weapon Amplification and Specialization are must-haves on just about every build anymore. Anything using Torpedoes or Energy weapons will benefit from these skill points. Since I was around for the Imperial Rift Set event, I also run that on my exotic builds which converts my Weapon Amplification into Criticals for my exotic powers. Now, in reality the Weapon Specialization is pretty weak (0.6% CrtH for the last point). I may drop this point someday.

Subsystem tuning (and power in general) is a tricky subject. As an Engineer, I get access to EPS Power Transfer, which adds 30 max and current power to each subsystem. Each ship also comes with power bonuses, and I am using Emergency Power abilities as well. I ended up choosing Warp Core Potential to add a flat 3 to each subsystem for a total of 12 (largest single +power per skill point). I also chose offensive because of the 4.8 power for engines trying to speed my ships up, and the 4.8 helps for my energy builds as well. This is a total of 9.6 power for the point. Improved Warp Core potential adds a total of 8 (2 per system), and adding to a specific system only adds 3.2 power, so significantly diminishing returns. I also like a lot of Auxiliary power for my exotic powers and the Web Cannon & Webspinner which scale strongly with Aux.

Exotic Particle Generator is fantastic because of Particle Manipulator. That means each point here contributes to all my exotic powers in flat damage and criticals. Since almost all builds have at least some exotic powers, these points are well spent. Even Advanced only giving 15 EPG means an extra 7.5% Cat1, 3% CrtH, and 1.5% CrtD, which is as strong as some Starship Traits (namely the CrtH). Exotic Particle Amplifiers also scale off of EPG, and slotting up to four of these on a build makes hitting 500 EPG all the more important.

Long Range Targeting Sensors is always maxed out on energy builds for me because it is the only source that reduces damage falloff with distance. There's no other way to get this, which makes it pretty hard to pass up.

Hull/Shield Pen for weapons is a tough one, especially since some of my biggest damage dealers ignore shields, and these skills translate to such a low amount of actual value, and they are only for weapons. Even if I was extremely focused on weapon damage, these would be near the end of the list for pickups because the value is so low. A single point is 1/2 a [Pen] mod, and all 3 is a single [Pen] mod. On the builds that need it, they have a huge amount of debuff already (5-10x per power), so these points are pretty weak.

Readiness is absolutely wasted because of the methods I use to hit global cooldown. On my exotic builds, I get there with Improved Photonic Officer, which buffs exotics and has 100% Photonic Officer uptime for cooldowns. On my Jorogumo and Tarantula, I use Aux to Batt plus some technicians for cooldowns. I benefit from Cold Hearted as a result. In both cases, I have fantastic cooldowns tied to other primary benefits. Where I don't use either of those methods, Boimler's exists and fills in all the gaps routinely.

Shield Mastery is always terrible. Ignoring a random hit once every 20 seconds is terrible, and none of the other downstream points help either.

Coordination is really solid for me solo, but also as part of a team. 2 of my builds use hangar pets, and all have summon clickies (Delta Reinforcements, etc.). As part of a team, I can't expect anyone to send the buff my way if I don't send it to them (Do unto others as you would have them do unto you, Matthew 7:12).

As far as unlocks go, there's usually either a pretty minor choice or only one relevant option. I don't push skill points anywhere just to hit unlocks. Battery Expertise can't be replaced.

Notes

Equipment is key here, and you'll notice I don't have everything to Epic. That's simply a cost-benefit, and I will get there someday. The majority of the damage and skill benefit comes from upgrading mark. Adding Rarity on Deflector, Secondary Deflector, Impulse, Warp, and Shields adds only the additional modifier(s), which in general are a small contribution to the build. 

The Nukara Mines are slotted for their holds rather than damage done, as well as Tholian theme. The Altamid Omni is totally replaceable as this is here solely for the +1% CrtH as well as the proc for extra Kinetic DRR. 

What is important is getting everything to Mk XV as the biggest bang for your buck comes from that upgrade. This adds a significant amount of Cat1 damage to each piece. 

The Web Cannon, for reference, when treated to a buff cycle of powers outputs a 50k damage blast, followed by 28k damage to every target every 0.5s for 12 seconds, which is over 600k damage. That's not even counting a critical hit!

This is by no means a budget build, but many of the key pieces were simply from running events or once inexpensive exchange purchases. I've been collecting pieces for this build since the Tarantula was a new ship and shared a low price point with the Vonph...

Notes

Since my focus is on the clicky powers and exotic damage, the Bridge Officer selections need to support that. Spore-Infused Anomalies (starship trait) keys off Anomalies and science powers, so when possible these were maximized. I also add several control powers to increase the uptime of Clicky consoles. It's possible that Delayed Overload Cascade will be replaced in the near future to further this goal. 

Tractor Beam is a "mule" power, useless on its own, but when combined with Unconventional Systems, it helps reduce cooldown on all of my clicky consoles. Delayed Overload Cascade is currently not the best power with how far it can fling enemies, but is a strong trigger for the Secondary Deflector. Tyken's rift is also here for the Secondary Deflector, and is used in the off cycle with Gravity well. It is stronger damage but no pull, and also an anomaly for Spore Infused Anomalies. 

Miscellaneous