I've been playing for a few months and Sci BOffs have not changed enough to notice (or that I've noticed if the have).
Having said that, I had the same question and settled on Sci, but I'm flying a Cruiser for solo PvE. I also have a Sci ship for grouping in PvE. I love the support role in MMOs so Sci was the choice, yet I love Love LOVE the cruisers in STO. So I make it work for me.
I think the dichotomy between PvE and PvP is the determining factor for you - where do you want to go? Then focus your decision to that end.
Engineers are essentially tanks... except for that Scis can tank pretty well, too, thanks to SciFleet and Scattering Field. The extra damage from Sensor Scan and Photonic Fleet are quite useful, and SNB is always good.
Devs would like a concise list of things that are broken and not working currently, so here's a short list for PvP: Neutronic Torpedoes, Ionic Turbulence, Surgical Strikes (including Faeht firing through cloak), PartGen stacking and CrtH being boosted to absurd levels.
1. The need for crowd control has gone up decently in recent content. Fleet actions and the "resurgence" of the high-mob fleet actions means CC is a bit more desired than before.
2. Remember that, especially in space, Captain type is only a small fraction of what you bring to the table - captain class only determines 4 powers and the effect of the 5th (fleet support X), your ship is 95% of your powerset. As such, a cruiser is a tank, period.
So, on those notes:
Since class means a lot more groundside, especially in a lot of the end-game content where you don't bring BOffs, I'd base class pick more on what you'd want when out of the ship.
In space, remember that the engie's 4 "unique" powers only benefit the player's ship, while the science captain gets an interesting mix of unique powers that are "shared", sensor scan benefits everyone shooting at the target, scattering field protects everyone around you, subnuking buffs away takes down a lot of an enemy's offense/defense, and photonic fleet adds a hair of offense to everyone, while the engie has what, 2 heals, a power booster, and a major resist booster that are all self-targetted only...
Well, with the upgrade announcement leaving NX and Connie fans in the dust again, can we restart / revisit the T5 Connie and NX threads - since they will no longer be "truly" endgame ships... (after we get the T5 versions, it'll be time to see them added to the T5U upgrade charts too...