If there's one kind of full length fanimation that could probably make it, it could be an anthology film consisting of short films by several animators. It would be similar to anthology films like The Animatrix, Batman: Gotham Knight, and Halo Legends. The film could be called "Equestria Chronicles", meaning each segment would take place within Equestria's history.
Each segment would be animated with a different animation program, excluding Flash and SFM. Such software would include Toon Boom Harmony (one puppet and one frame by frame), Anime Studio Pro, TVPaint, Digicel Flipbook, OpenToonz, Autodesk Maya, and Blender. Other programs would be used alongside those animation tools. Each segment would look extremely professional in terms of animation quality, and would make any fanimation done in Flash or SFM pale in comparison.