Well some of the same dev time would be involved but there's just a whole lot of factors that separate them.
Adding a custom move means a new visual effect for the attack, some programing/frame changes to alter the attack's properties, and some (relatively) simple balancing tests.
New characters means a new model for each game, one of which is a detailed HD model, an entire new movelist (jab tilts smashes aerials grab/throws special moves that aren't just tweaks of existing special moves final smash), a crap ton of animations and facial expressions for being hit/grabbing ledges/running/walking/swimming maybe/jumping/double jumpy/tripping on banana peels/being hit by varous effect attacks ect. ect. ect., likely extensive research into that character and every game they've been in quite possibly including playing the games to get a feel for them, physics traits like the character's weight floatiness traction and speed, potentially working out character specific gimmicks, a new CG trailer if that character is a newcomer, likely a home stage for that character and if they're from a new series a bunch of new music, voice work which requires pick and hiring a voice actor, determing sound effects for every action, likely extensive back and forth with the company that owns the character if they aren't from vanilla Nintendo like with the Pokémon characters, little extra things that playable characters get like an end of classic mode montage multiple trophies minigames if those end up being individualized again official artwork a website page a Kirby hat ect., and most importantly a much, much more rigorous balancing process. And probably other things I'm not thinking of/not aware of.
And balancing gets a lot harder the larger your cast gets, in a fashion that's non-linear, and things tend to become a real mess when you get past 50ish characters, especially if you're adding a lot of new ones all at once. I don't think this is nearly as acute a problem with custom moves, though it still is to an extent.
To say nothing of the fact that the effect that they have on the game at large (giving each character more options vs. just having more characters overall, among other things) is just wildly different, though I guess that's what the question was addressing.
I just think it's a bit far into apples and oranges territory. Also, I really don't think cutting the custom move variants entirely would give us more than just a couple extra characters. I pretty positive there's no way we'd be getting 60-70 characters either way.