MBTiles is a specification that defines storage of tiles, rather than data. Even if the scope of the spec expands to include vector data, the expectation is that that data will be tiled, rather than in its native form. Another standard will be necessary to store raw data and styles of the sort that you could use to generate an MBTiles file.
SQLite natively provides all of the spatial queries we'd need to spatialize some of this spec - Spatialite only adds projections support, which is not within this spec: we support a single projection.
Spatialite is also extremely restrictively licensed in relation to this project, SQLite itself, and the products that we're building. There are no plans to shift it from its current license, and this limits its adoption.
While MBTiles requires only SQLite, adding the linked, compiled dependency of Spatialite would make it severely difficult to use in most environments, like from Objective-C or Python.
I believe that using spatiale could give many advantages