I never even considered one might play Undertale where you only kill some people but not others, the game doesn’t really ever incentivize you to do a “mixed” run.
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…
The first time I played, I believe I killed only Undyne and none of the others.
I couldn't easily figure out her mercy gimmick, and I understood her to have agreed to live by the blade, and by extension, die by it. Given her relentless hunting of the main character it seemed not inappropriate.
After subsequent playthroughs my thoughts are more complicated.
The funny thing is, not only are there multiple Neutral endings, Toby actually wrote different variations of them for almost every possible combination of boss kill. They range from "you know, Alphys wanted to talk to you about something" if you killed nobody, to "if Sans ever figures out how to leave the Underground, he will end you". The latter is what you'd get if you misinterpreted "Genocide run" to mean "kill everything you see", which isn't quite it.
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.
It takes some really serious farming to accidentally find genocide route and then not exit it my mistake. Most players blindly treating Undertale as a regular RPG would simply kill the enemies they encounter (which is not enough to trigger genocide route), maybe regret it along the way, and eventually get a neutral ending plus the hints to try pacifist.
It's clearly the intended progression, since the second playthrough then changes to reflect the fact that the game "remembers" your first one.
