I think it's safe to assume that CLANNAD is eligible for Smash. If Makoto (Danganronpa), and Monokuma can be playable, then I guess Tomoya (Clannad) can be playable as well.
There are actually a number of obscure 3rd party franchises that are currently represented in Smash, including Bayonetta, Fatal Frame, Mystical Ninja Goemon, No More Heroes, and many more. Obscure 3rd party franchises can still get representation, however, they are typically better off without getting any playable characters. Not to mention, I also support Saber (Fate/Stay Night) as well, but for Tomoya (CLANNAD) on the other hand, I want him to be a mii costume, spirit, or assist trophy at most.
You are correct! Fate is better known as an anime than a visual novel. However, it still originated as a visual novel. Thus, Saber (Fate) is still viable.