Hi Biggles!
Yes, you are right! A piano is not a flight simulator!! haha, just joking
Well, the pythagorean intonation IS very theoretical. Understanding the incomprehensible theoretical framework of intonation does not help, especially on the piano, since it is a tempered instrument.
One of the reasons it has been tempered, is because then the uppertones (fifth, octave, etc) are resonating effectively with the root note. That is, you can theoretically press any key combination, loading a sample in midi, no time.
An uppertone is the upper resonance of the root note. (fifth, octave, and if I remeber correctly ninth, or 13th. a 13th in the key of C major is A).
One of the reasons Neil Young uses the ninth chords (which is a root, a third (minor or major), a fifth, and a ninth, which in the key of C major is a D), is because of the uppertone resonance. You can check out this dark chords for instance in Neil Young, Cortes the killer. The studio version.
You are also right, that extensive scale exercises are designed for untempered instruments, like bowed, or plucked, like a lute. Even there, too much scale, mindlessly, are meaning more harm then good.
In piano, the basic notion is that you have to scale softly with the first and second finger, pressing with the first, then the next white note (C major) with the second finger, and then the third white note with again the first finger. Do this, till you reach the 8th note (the octave of the root), where play normally.
Yes, simple tunes and exercises are better for piano technique, you'll understand why. But, I'd recommend a classical education booklet, like easy piano sonatas (Handel and Bach, Scarlatti, etc) after a while.
Why? Because it is very important to follow the fingering notation in the first few months. I mean, there is a number above the note. That corresponds to a finger, with which the note should be pressed, if strictly following the classical etude, or simple piece.
Why? Because of the hand shapes.
Hope that helps, best,
Krisztian