Well it's not only Lucy as a non-prisoner present in the present. The doctor is here, too.
Still, some mysteries already besides the obvious "How did they get here/Where have they been?" The cop's grandfather seems to spend a lot of time in the hospital ward, with them taking his blood. The prisoners, for seemingly not knowing anything, seemed to adapt to 2012 damn well. If Lucy and the doctor reappeared, they don't seem to be able to provide much info. Hauser looks mighty fit for 70+. Hurley's regained all the weight he lost on the island.
The bad guys are really shown as being awful, which is honest for them being sent to Alcatraz. Who couldn't identify as just being out for the day...when suddenly a sniper fires. Disquieting feeling watching that.
Oh, and they have that mystery key from Flynn (who was killed in the first ep), and elevators that require a key to access? Coincidenza?