He not is.
He is not.
Using the second method, you have to listen to the third word 100% of the time, instead of only when "not" is used.
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There are a lot of things going on here even for something so simple as where to place negation. There are general linguistic things going on, plus English specific things.
In general, anything goes in grammar. OK not -anything-, but quite a lot you wouldn't expect. Some languages have Subject Verb-Object order (or SOV):
The man catches the rabbit.
This seems entirely logical to me, and anything else is stark raving lunacy. Except some languages are Subject-Object-Verb. Classically, Vulgar Latin has this:
homo leporem capit. ("Man rabbit catches")
SVO and SOV are the most common languages in the world, but there are even VSO languages, like Irish.
Glacann an fear an coinín ("Catches the man the rabbit")
(as the Germans say "Die Iren sind irren").
The point of this so far is that the order of pieces can vary. None are illogical. It's in some sense a style choice that just happens to be preserved in a community so it feels like it is eternal truth.
So whether you put the negative marker first or second, -something- is going to be left unsaid.
"He is..." what is it? "He is not..." OK whatever it is it's not that, but what is it still? That's the current way.
"He not..." what's going to not happen? "He not is..." OK, but still what is it that is not?
It kinda turns out that English does -both- kinds of negation.
The man does not catch the rabbit.
The marker for negation here comes before like you desired (that pesky 'does' has an interesting history called 'do-support'). But that is not 'logical' it's just one way of doing things.
French also has interesting negation. It used to put 'ne', essentially the same thing as English 'not', in front of the verb.
L'homme n'attrape pas le lapin
(the 'e' in 'ne' is elided because it's easy to do). But what is that 'pas'? It literally means English 'step' and is sort of like 'not one step' as an intensifier.
And over the years, colloquial French has tended to -drop- the 'ne' entirely. You'll hear important people in the news saying
L'homme attrape pas le lapin.
So even though 'pas' literally means 'step', it doesn't matter what it literally means because it is the only thing that marks negation in the sentence so it totally means 'not' now.
That's pretty much it. You just gotta get used to the idea that:
Language wasn't designed by one person who is trying to optimize one of your pet criteria (let's say 'continuous partial prefix interpretation'?)
Language changes. Styles change, order of words change, vocabulary changes.
Language does a bunch of other crazy stuff you wouldn't expect. You just get used to it.