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.
The first we heard of getting new PvP maps "soon" was in August of 2010. We're consistently told something will be coming with the "next" update. Absolutely nothing has come to PvP since launch.
I think it's finally time Cryptic stopped stringing us along, don't you?
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...
50: S'Leth/Eurthyr/S. Dareau/Ardrian/Krudge/Annlova Not: Jadja
Still at it. CBS "restrictions" fell by wayside with freebie Breen. Time to re-examine ENT and ToS at tier 5, repurpose the Connie into Sci and rebuild an Akira escort into the "NX". 6 "eras", spread evenly over all the classes...