This is a simple experiment I tried using Camel Audio Alchemy.
I took a guitar sample and imported it into Alchemy's additive synthesis engine.
The file was analyzed and resynthesized using 32 partials. Alchemy allows to create "pitch profiles". I quote from the manual:
"Each profile definition requires a pair of files with identical base names and different extensions: the profile corresponding to a knob value of 0% has the extension .csv, while the profile corresponding to a knob value of 100% has the extension .csv2." (csv stands for "comma-separated values").

I created 2 files of this kind (boggling.csv/csv2), as you can see from the picture below:



The grayish one on the left simply tells Alchemy to use the usual harmonic relationship among partials, the one on the right is an arbitrary one I chose to make sure that it sounded different from the first one. It is clearly inharmonic!

I quote again from Alchemy's manual:
"The Pitch knob applies a variable offset to each partial pitch. The nature of this offset depends on the setting chosen in the Pitch pop-up menu directly below the knob".
So, it is possible to dynamically control the partial's "alignment". That's what I have done while playing an arpeggio based on the simplest harmonic progression of Western music: I IV V I.


(Click on the picture to watch the movie)

Look at the knob on the bottom right side: as the Pitch knob moves from 0% toward 100% the familiar progression gets increasingly out of tune and vice versa.

What's the conclusion of this experiment?

A quote from http://en.wikipedia.org/wiki/Timbre helps explaining it:
"William Sethares (2004) wrote that just intonation and the western equal tempered scale derive from the harmonic spectra/timbre of most western instruments. Similarly the specific inharmonic timbre of Thai metallophones would produce the seven-tone near-equal temperament they do indeed employ. The five-note sometimes near-equal tempered slendro scale provides the most consonance in the combination of the inharmonic spectra of Balinese metallophones".

As a researcher of alternative tuning systems (to 12tET) I think the road to follow for their advancement is the creation of new classes of instruments capable of playing them in a consonant way. Personally, for this purpose, I think about the creation of digitally resynthesized instruments.