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I'm personally quite fond of my Palatine Multi-Mission Reconnaissance Explorer, even if it isn't meta.
What exactly are you looking for in a science ship?
Buffing/supporting other players is kinda pointless in STO due to the amount of damage a well-geared and well-flown player can put out.
Most part if you're looking to do sci, it's mostly just "doing damage" but with space magic instead of ship weapons.
You can get the Nautilus Temporal Science Vessel. It's a future ship by default but acquiring the Daedalus Temporal Science Vessel (37.5k refined dilithium - see the ship vendor) will allow you to use the Daedalus' skin on the Nautilus. That's the only Science ship with a TOS skin though.
You can use the TOS material on newer Science releases - the Grissom/T6 Oberth and Somerville can both use the TOS options, although they're not explicitly TOS-themed.
The "Temporal" ships.
The TOS aesthetic will be gated behind a paywall tho and if I understand that menu right you first gotta buy the ship THEN pay extra for the aesthetic.
All the low-tier ships are only available for Dilithium now.
Correct, with a couple of exceptions, all of the T1-T4 ships were removed from zen store a few months ago. There's still a couple (T1 Connie, T4 Intrepid, T4 Defiant) that are available for zen ONLY as part of a bundle.
As for the original poster's question, my suggestion would be, if possible, the Legendary Intrepid, though it does not (to my knowledge) have the TOS aesthetic, it is, I believe, the highest-output science ship around.
The Verne Temporal Science Vessel, the Risian Weather Control ship, (last year's summer event) the standard "Pathfinder" T6 Intrepid, the Scryer, and a few others are comparable to each other at the next level down.
Not sure you're right there. You'd want to use the Commander seating for throwing out anomalies, making the Commander station irrelevant compared to the Verne's Temporal seating. Verne is probably the best sci ship, with the Eternal being a close second.
Scitorp is usually Command (due to Concentrate Firepower), so you'll want the Titan or something with Command seating.
I shouldn't have said "All the low-tier ships", sorry. Ik some are still available via packs. Not sure why I didn't remember that.
It's not all just about the BOFF seating.
The Legendary Intrepid, being a Miracle Worker spec ship, gets an extra universal console slot, which will take anything, so you can stick in an extra science console... all else being equal, that would make the damage output a little higher. It also has a hangar, which some of the others listed do not.
The best science ship is the Verne, followed closely by the Eternal. ImperatorPavel was spot on with that. Verne is technically a lockbox ship, but you can get it from one of the Mudd packs that comes around from time to time. Eternal you can get as a ZEN ship quite easily.
Science ships are primarily about throwing out apocalyptic anomalies. You can do other things with them, but you're basically making a gimmick build at that point.
Legendary Intrepid is hardly the highest output - it can field one additional science console but that doesn't significantly shift the damage upward. Most of the consoles that boost exotic damage are universal, not science-locked. It's not a bad science ship, of course, but it's certainly not the best.
Seating is one of the most important things about a ship as it determines your access to abilities, both in number and magnitude. I'm pretty sure we've been over this with you already in another thread. MW ships are pretty great, and they tend to be among the best for weapon builds, but Temporal ships are better for science as the support mode gives more exotic and control bonuses than you can get from a single console.