The movie, from my understanding, was supposed to be the first installment of a trilogy. Because of the poor ratings, that trilogy will probably never be realized.
In regards to what the movie was actually about: It is about change. John Logan had written a beautiful story that was supposed to be about change, about the reality of a military career. This movie was supposed to focus in on character relationships and careers taking their lives in different direction. It's plainly obvious just from reviewing and watching the deleted scenes, which were, ironically, mostly character moments. The most moving scene, imho, of the entire movie ended up getting cut and sent to the bonus features as grainy, unfinished film. It's a scene where Geordi and Worf are cleaning out Data's quarters, both carrying on in a very gloomy silence. In this scene, it is basically a journey down memory lane as you see the quarters a mess after the battle and laying about are a bunch of items that are recognized from the TNG series, posessions that helped to shape and mold him into who he became. At the end, you see Spot climb out from a bunch of toppled furniture and jump into Worfs arms. He says "I am not a cat person." Geordi smiles, and seems to tear up a little before he replies with, "You are now!" Not to mention that the alternate ending was so much more wholesome to the story. We meet the new commander, Commander Martin Madden, as Riker is leaving to assume his posting. Riker plays a little joke on him which was really funny. In this shot, we don't pan away to credits seeing the Enterprise helpless in dry dock, we see it going cruising away at impulse, fully repaired and ready to go. Basically, we see life on the Enterprise, changes and all, continuing on with business as usual. This scene was very, very well executed and very pleasantly done. If they had kept the deleted scenes and kept the alternate ending, I think the entire tone of the movie would be different.
My honest, genuine opinion is that the reason this movie failed is because Stuart Baird was a disaster. His calling is EDITING. This man needs to leave directing alone. He's smug, he's arrogant and frankly from what I could see of him, he's really weird in that creepy kind of way. I blame him, and him solely for the failure of Nemesis. John Logan had a fantastic story that was a fantastic send off for this crew, but Baird decided that he didn't care, he would go in and completely change the pace of the story because he thinks he knows so much about it. You want someone to blame, blame him.