Sometimes you have to keep your expectations on the low side. Excluding the Mii fighters, having 60 fighters total would be fair enough, but if cuts have to be made during the process, then some of the clone characters may have the greatest risk of getting the boot.
Honestly, I've never understood this logic. If cuts are made due to time constraints, why would the clones, the characters who require the least effort, be the ones to go?
Obviously, we had clones cut in the transition from Melee to Brawl, but circumstances were a bit different then. Sakurai was actively differentiating every clone he brought back from their base (Luigi, Ganondorf, Falco) and likely opted to cut Roy and Dr. Mario because he didn't have time to do the same for them. (Or, in Dr. Mario's case, because it might have been awkward to have both Marios for Subspace.)
In the transition from Brawl to Smash 4, the characters that were cut due to time constraints were semi-clones (Lucas initially, Wolf) and Pokemon Trainer's less popular two Pokemon. The semi-clones were, frankly, only cut because people valued fully unique movesets more than the 75% unique semi-clone movesets.
Semi-clones being cut actually saved time and resources because they were mostly unique. In the transition from Melee to Brawl, them being cut saved time and resources because Sakurai wanted to de-clone them as much as possible and didn't have time.
This time around, there's not really a reason to de-clone the clones we have. Lucina is Marth without the tip, which doesn't take much effort and is still unique. Dark Pit is almost entirely the same as Pit, but exists because Sakurai wanted a different Final Smash; he may not change at all outside of that. Dr. Mario is just a Melee throwback, and has no real reason to be further decloned than he already is.
Cutting any of those clones saves such a small amount of development time that it's not really worth it. You could save more time by cutting a unique character (say, the Mii Gunner while keeping the other Miis) and come out with more characters than you would cutting all three clones.