1. The movie as a whole is very smart. A lot of movies (kids movies in particular) have nerdy main characters. What we DON'T see all that often is nerds getting to ACTUALLY be smart, as opposed to having their smartness faked via technobabble ("if we adjust the phase emitter we can increase the power of the shields and save the day wooo!!!!"). I'm not sure the devices that Hiccup makes would actually work but a lot of thought was clearly put into how they might work and I found them totally believable. We really get the sense that not just anyone could have did what Hiccup did, and what he did took time and intellect to study and prepare. I love that Toothless couldn't fly straight with an injured tail, and that they not only had to make a fake tail but build a device to change the position and then learn how to work together to operate it.
2. The two headed dragon was particularly neat. It actually works the way I always thought dragons probably should (breathing flamable gas and creating a spark to ignite it). And seeing the twins flying on it at the end was funny.
3. Having Hiccup lose his leg at the end was pretty neat. The friend I saw it with didn't like seeing a kid in a movie lose a leg, but I thought it was a very good way to to introduce children to the fact that going into war is going to have consequences without having to actually kill off a main character to showcase it. And it had a very nice symmetry - the dragon loses his tail at the beginning and Hiccup helps him recover, and then Hiccup loses a leg and needs the dragon's help to walk at the end. I've been reading some blogs on the portrayal of handicapped people in movies and this film definitely had some good stuff in that regard.
4. I think this is the first 3D movie where I felt that the 3D was worth paying extra for. A lot of scenes in the beginning actively used 3D to emphasize facial expressions which enhanced the emotional impact of the scene rather than distracting from it. I was still a little disappointed that the big epic scenes near the end did not use the 3D to its full extent. It basically was "realistic", which is okay I guess but I for one miss the 3D where stuff actually jumped out at you. The giant canyons and the huge dragon both could have used some exaggerated perspective to emphasize how huge they are. Still, I found the 3D worth the money I paid extra, more so than I did for Avatar or Alice.
5. Minor quibble on a related note: I like that the girlfriend character gets to be a badass, but honestly we've come far enough that that's a cliché unto itself. I didn't like that despite that, she essentially is a background setpiece for the main character's benefit, with no particular arc of her own. She spent most of her life trying to be the best dragonslayer in her class, and suddenly the entire dragonslaying occupation becomes meaningless. Granted, everyone then gets to ride dragons all the time, which is really frickin' sweet, but still, it'd have been nice to see how she dealt with that. Also, having a job in the climax other than to stand around and be supportive of the protagonist. (In isolation, I don't think the movie was all that bad in the feminist-regard, but overall the "scripts-are-clearly-written-with-male-biases" is still enough an issue in Hollywood that I feel obligated to point it out when it happens).
6. And then on the other hand... "Here son, wear your Mom's left boob on your head. Now we have a matching set!" LOL!