First, perhaps because it was 3D, I found my eyes being drawn to various things that I had never noticed before. Small things, like how there seemed to be a lot of folks walking around on Tatooine with full spacesuit helmets on. I noticed for the first time that Anakin's ship doesn't leave any marks on the floor when it crashes into the droid control ship. I focused on the people standing behind Jabba and looked at the different designs for each Gungan.
I also walked away with new questions. When Qui Gon is going into town, why does he take Jar Jar with him? At the climax of the film, why does Nute Gunray say, "This one is an imposter!" in regards to the disguised Queen Amidala (why did he think she was the queen at all, in other words)? If Qui Gon has 20,000 republic credits, why didn't he just book passage off of the planet with someone like Han Solo (republic credits may be no good on Tatooine but a transport vessel wouldn't just stay on Tatooine, would it?)?
Additionally, I picked up on how many moments there are in the film that are completely unnecessary to move the story forward. These moments seemed designed to do nothing but show off visuals. This is particularly striking when compared to similar scenes in Ep. II and III. For example, ship lands and take offs seem to take up more time than necessary (in the sense of film making). The scene where the Sandoo Aqua Monster eats the Opee Sea Killer... do we need to linger for a few seconds to see it rip it in half? Do we need to watch the Naboo fighter ship after it's shot down... all the way to the ground?
Seeing a movie on the big screen definitely opens me to a different perspective than watching the DVDs. Just the size of it allows me to pick up on small details that I may have missed previously. Which, in the Star Wars world, I can never get enough of.