Continuing an idea from the last post, about how inter-pasuk gaps are forbidden by Masechet Soferim but implemented lechatchila by the Rema, and how these gaps were used to designate something that it not obvious without punctuation:
For a while now I've had an idea, but am not entirely sure it passed halachic muster. I think it does, but have not done enough research (such as learning through the relevant gemaras, Yerushalmis, masechet Soferim, as well Rishonim and Acharonim) to make such a determination.
My idea is to use elongations of letters (which is permitted, and is used at times to justify rather than right-align sifrei Torah) as well as the crowns (tagin) upon certain letters to encode extra information. One can vary height of tagin, as well as their lean (left, upright, right). This can be used to encode trup or nikkud, such that a baal koreh on the lookout for this can know where there is an esnachta, or a silluk, or where it is es instead of eis. It is just a matter of combining these features into a system, implementing it, and remembering it.
Indeed, the conspiracy theorist in me suspects, with little proof, that this was the original intent of the tagin. The facts of the matter are that (a) our tagin are smoothed out in terms of varieties, but there were all sorts of traditions about the tagin on various words, which is no longer implemented; and (b) Rabbi Akiva darshened these crowns.
My suspicion is that these crowns initially did in fact encode some information, perhaps vowels, perhaps parse structure for the pesukim. And according to midrash, Moshe put them on but did not know what they meant. Perhaps Rabbi Akiva analyzed the tagin, and found and developed a system, which revealed the meaning conveyed by the crowns. And while our orthography of trup perhaps did not exist in Talmudic times, perhaps these were somewhat akin.