Pacifist is more like a puzzle game, and I didn’t find it all that challenging at all.
If you go the “kill only some people” route, I don’t think you would ever really be strong enough for this to be fun due to not levelling up enough to keep up with later stage enemies. So you’re going to be heavily incentivized to go full pacifist to bypass levelling entirely or genocide to get enough levels. Then of course you’ll hit the wall at the end…
It's clearly the intended progression, since the second playthrough then changes to reflect the fact that the game "remembers" your first one.
My guess is that Toby's intent was for you to play the game normally, get one of the many, many different Neutral endings, reset to get the Pacifist ending, and then a few years later come back to Genocide after hearing about this weird route where you get to fight the other font skeleton.