It's an oversimplification to suggest that scales are based on the harmonic series. Many instruments have slight non-linearities in their overtones, and intervals that sound consonant aren't usually mathematically perfect. E.g. pianos don't even have perfect octaves. The major and minor scales seem to be based on very specific ratio sets, not on the general overtone series.

But 12TET has 12 tones for a very practical reason - instruments with more tones are difficult to build and damn near impossible to play, because human hands are only so wide and finger movements have limited precision.

There were experiments with more tones per octave back in the middle ages, but the idea never caught on because the musical benefits aren't obvious. So 12TET is a 'good enough' compromise between flexibility and expressiveness.

Performers on instruments with an infinite pitch range vary their pitches anyway. Intonation problems drive conductors insane, and the reality is that orchestral and choral pitches tend to drift slightly towards consonance and away from the nominal ET ratios.

Of course, with a computer you can do what you like. Here's some recent microtonal music written with SuperCollider:

http://composerprogrammer.com/pitchdeviations.html