What parts about the plotline do you not understand? In the third "episode," things are explained in detail. I think you might understand better after watching the classroom scene in that. It's not exactly simple, but it's explained. It might be better to watch UTW's release, which is all four episodes combined into the movie format they were meant to be in. Nekomonogatari actually impressed me by being much more like Bake than Nise after episode 1.
Also, anyone who likes the -monogatari series should watch Katanagatari. It's an excellent series, but I won't explain why I prefer Bakemonogatari since I don't want to spoil anything.
EDIT: The ending's message really tied into the similarities between different arcs in the -monogatari series. They all have a pretty overarching purpose/message that is stronger than I previously thought. (spoiler (?): It's basically: You're the only one who can deal with your own shit and carry your own weight. Anyone who tries to use the supernatural to cheat their way out of life's difficulties gets bitten in the ass.) The seemingly lackluster anti-Disney-esque-happy-ending where Araragi basically said that there isn't a magical way to solve how much your life sucks and fix your problems, and he's not going to be some hero who makes her life great for her, man... it's making me want to rewatch Bake again. I know the messages for Senjou's arc and Kanbaru's arc were pretty much the same thing. Senjou got her weight back both literally and metaphorically. Araragi basically helped her get her normal problems and normal damaged life back so she could bear them herself. This is very contrary to what anime usually does and usually has as a message. In most anime, the protagonist defeats everything against all odds, saves everyone, and fixes other people's problems completely, for a happy ending. Araragi doesn't even fight, he uses logic and still needs to lose a little to make things "right"... but right in the sense that people have control over their own lives again and can begin moving on. The people Araragi helps cannot be passive like damsels in distress. Their problems with Oddities stem from personal psychological problems, their emotions, or mistakes. Instead of Araragi fixing their personal problems for them, he helps them get control of them again. Oddities make them go out of control, basically. The only time Araragi used violence to solve things by killing, he had to pay for it. (Kizu) (spoiler alert: It was basically like: No one can win, and no one can be happy. They had already gotten into a mess where there was just a certain amount of suffering that needed to be had. Maybe that changed Araragi.) Anyway, the messages of individual arcs are pretty obvious, but I never thought that they all go by pretty much the same formula. Is this all obvious, or all wrong? I don't even know, Nisio does some convoluted shit. Katanagatari's ending is VERY similar for its message, but in a way that involves the viewers... kind of. At least for me. And it didn't feel good, but weeks after being pissed I started respecting it a lot more. I felt awful because I love Disney happily ever after endings. Or you could go for a tragedy. But it was neither, it challenged the way "the moral of the story" is delivered and seen. I realized this theme more now because it was in a very pure form for Neko. In other arcs, it was more subtle, and I didn't think back to relate it to previous arcs as much. They felt similar in emotion and resolution, but still separate. I guess I'm just viewing it as a more unified work in terms of plot structure now. One thing I've always been sure of in terms of the reoccurring theme is that Araragi helps people gain control over their problems again, Oddities make their problems go out of control... but Araragi doesn't solve their problems for them. tl;dr It's a series about realization and acceptance of oneself. About one's problems and one's personal responsibility regarding them. Something else that's interesting is how Araragi has this desire to die meaningfully, has tried it multiple times, and has a martyr complex, but I'm already making this post retarded and rambling. I think a lot of these messages come on strong in Kizu, which has heavy moral implications, and I wonder if the philosophical debate at the end of Nise ties into this stuff.