Just got back from a 3 night Dream cruise (first Disney cruise) and while everything was amazing, the check in process definitely has quite a ways to go. We got there around 1:30 (our boarding time was ~2:30 from the online check in I think) and the terminal was swamped. All the switchbacks leading up to the check in counters were full and behind that was an unorganized mob of people trying to merge together from the ground level and parking garage entrances to the terminal. So they definitely have something to work on there.
Didn't really understand the purpose of online check-in (because best I could tell, the process in the terminal doesn't change if you did it or not). It doesn't appear to function like a resort check-in, where there is a separate line. As stated earlier the check in time given to you isn't enforced. The only thing about it I guess is to try and do it as early as possible, because I imagine the crowds earlier in the day are more manageable.
That, and if you are transporting yourself to the terminal and parking in the deck, leaving your luggage at the curb before the garage is the only way to get your bags on the boat without you manually bringing them through the aforementioned process yourself. You can't hand them off in the terminal to the check in agent, and the folks directing traffic into the terminal don't make it clear that this is the only way to not have to drag your luggage through the terminal.
That being said, once everything was in the room the trip was awesome from then on out and we only would have a few things to nitpick about otherwise. But we will definitely do a bit more planning on the checkin process for the next one.
Quick edit: Another tip, the first time you get on the boat there will be a huge wait at the elevators closest to the entrance. Do yourself a favor and use the aft or forward elevators, because I imagine they are significantly less crowded. For some odd reason they don't distribute the guests among the 3 elevator locations on the ship, though I imagine it would be less of a issue if we didn't have our luggage.