All of the characters are included. 103 total stages are included, which does not include every stage but includes the vast majority. Off the top of my head, it seems they cut some of the traveling stages with heavy platforming, ones that lost functionality (like Miiverse), ones that are similar to later stages in the series, and perhaps ones incompatible with Ultimate's features such as Stage Morph (this last point was inspired by a YouTube comment I read on this video).
The video I linked there lists every stage cut. Despite the commentary of the video, I'm pretty sure no additional stages were announced after that point. That would mean that 15 stages were cut.