You have the basics to a decent build here, but here are my suggestions:
1.) You should move away from Aux2Bat. It ultimately does more harm than good as it uses two valuable engineering boff slots, three doffs slots, and kills your auxiliary power severely limiting your healing and any outgoing exotic damage (FBP, for example). Your best option for managing your Cooldowns is to slot Strategist with Threatening Stance on thus triggering "Attrition Warfare," which will automatically reduce cooldowns when you select a heal ability. This is easily triggered by using Aux2Sif in your keybind rotation. If you don't yet have the Strategist tree filled out, you can use the Reciprocity trait from the Phantom Intel Escort for your CD management. At any rate, you should consider spending some time filling out the Strategist tree to use as a secondary.
2.) You could re-work some of your boff slots/abilities for much better results. Ultimately, this is up to you and what you plan to do with this build (Tanking, DPS-chasing, etc.). I would recommend, at the very least, slotting at least one attack pattern in your tactical abilities. For optimal DPS, pairing an Attack Pattern with FAW rotations is essential. You should also consider running Aux2Sif in your Commander Engineer, as it will easily trigger Attrition Warfare and provide a good amount of hull healing. Aux2Sif3 would obviously provide the greatest amount of hull healing. If you want to look at some other builds for your inspiration, I'd recommend you check out the DPS League's builds. They have good set-ups for all three Odyssey cruisers. https://www.sto-league.com/federation-fl...-odysseys/
3.) Since you're using fleet weapons, It's better to run [Dmg]x3 [CrtD] than [Dmg]x3 [CrtH]. For more information on weapon mods, check out this
. If you're wanting to upgrade out of Fleet weapons, it's recommended to acquire crafted beams with the [CrtD]x3 [Pen] mods. Please not that for Tactical captains [Dmg]x3 [Pen] mods are superior, but [CrtD]x3 [Pen] weapon mods are better for Eng/Sci captains.
4.) As for the Flagship consoles, I would argue it's beneficial to run at least 2 of them, but I would not use the full set, as you can use the leftover 2 slots for better consoles. Here's some consoles I'd recommend:
Tactical: Vulnerability Locaters with [AP] mods boost Antiproton damage slightly higher than the equivalent AP Mag Regulators at the same mark and rarity. Additionally, Vulnerability Locaters provide a slight boost to CrtH.
Science: Plasma-Generating Weapon Signature Amplifiers/Nullifiers with either [DrainX] or [EPG] mods. DrainX boosts your draining abilities, whereas EPG provides a boost to Exotic Damage.
Engineering: Plasmonic Leech (Universal) This can be found on the exchange for about 14 million EC (as of 08/01/16) and are worth every penny spent. In short, they're essential for just about every beam build as they drain your opponent's power and adds it to your own power levels. Also, if you have the Lobi, you'll want to get your hands on the Bio-Neural Infusion Circuits for 200 Lobi. This adds a significant amount of Critical Severity and Hull capacity once you get it to Mk XIV Epic.
5.) As far as Space sets are concerned, you should acquire the four-piece Iconian set (Engines, Deflector, Shields, and Core) from the Iconian Reputation System. That being said, I'd highly recommend you wait to grind any reputation set until you've hit Tier 5 in all your Reputations on you Temporal Agent (if you have one). The award for completing is the ability to craft any reputation item at Mk XIII Ultra-Rare instead of Mk XII VR. It goes without saying it's worth the wait if you take the time to work on your Temporal Agent.
In response to your final question, even though Tactical Captains *generally* have a higher-DPS capacity than Science/Engineering Captains, it is definitely possible to do more than 100K DPS if you're not a Tactical Captain. Check out this 132K Tholian Tarantula Engineer build and this 108K Eternal Science Torp build.
If you have any further questions, please do not hesitate to ask.