Here is the difference for me. How to Train Your Dragon 1 & 2 were fine films, but they did not challenge or do anything new. They were well crafted with solid characters and fun stories, but at no moment did I feel I was watching anything special. Anything that moved me as a person.  Now, there is nothing wrong with a fun film, and it is certainly far better than forgettable films like Shark Tale or Over the Hedge. DreamWorks has learned that its old style of "pop culture references, act hip and get big name VA" held them back from making good films.  How to Train Your Dragon avoided all those pit falls and is big part of why it is good.

Now, compare that to the end of Toy Story 3, a film on the surface about living toys has a deeper meaning on life. The toys represent childhood, and so many of us struggle as childhood dies and is replaced with adulthood. It is a bittersweet moment in our lives when we are faced with letting go and moving on. When Andy looked at Woody the pang of cherished memories and sense of loss it elevated that film beyond just being fun (which it was) and into introspection of life.  This theme is tied through out the three films, with the Toys own mortality being their main opposition.  To be tortured by a child, to be unloved and treated as museum piece, to be replaced and forgotten.  The toys live with the fear that their existence is tied to another, and it is only at the end of 3 that Andy appreciates how much of his own life is tied to them and what he is giving up. This is tempered that he understands that this is part of life much in the way his mother is letting go of him as he goes off to University to start his own life.  It was beautiful and it did all this not through heavy handed exposition, but nuances of animation and expression of emotion.  

To me a good film is one I enjoy. A great film is one that I enjoy and makes me think and/or feel.  We all have our own feelings on the issue of story telling, certainly take no issue if you enjoy something more or less than I do. Just my two cents as to why Pixar holds a special place fear it is losing when it makes more superficial films.

Well the first How to Train Your Dragon movie was one of the first CGI animated movies that looked really good in 3D.

I cannot speak to that as I get bad head aches when viewing films in 3D so never watched it in that format.  I will say from a technical perspective animated films of recent years have been impressive to me from nearly all major studios.