It might help some if we knew the technical meanings of [face=SPIonic]fro/nhsij[/face] and [face=SPIonic]sxe/sij[/face] in your Byzantine philosophical prose.
That said, I'll hazard what I can:
arkadi wrote:1. *if not for the comma*, the only possible subject here would be "schesis", since it is the only noun with the article;
Although there are many conditions under which the article may be omitted, the basic rule is that the predicate noun does
not take the article. This allows one to distinguish subject from predicate. I would agree that, without the comma, [face=SPIonic]sxe/sij[/face] is the grammatical subject.
arkadi wrote:2. as the phrase stands (i.e. with the comma), the only possible subject is "phrone^sis"?
I suppose the comma does help shift the grammatical subject to [face=SPIonic]fro/nhsij[/face]. But I think the subsequent [face=SPIonic]me/n[/face] is even more important in this regard. This use of [face=SPIonic]me/n[/face] 'solitarium' is often seen
with anarthrous substantives. It emphasizes the preceding word. The sense is something like "And (Even?) prudence - for its part - it is,....".
arkadi wrote:3. If so, how does it differ in meaning (if at all) from:
"Kai he^ phrone^sis men estin he^ schesis· ktl." ?
The sense here is one of identity. That is, this construction presents [face=SPIonic]fro/nhsij[/face] and [face=SPIonic]sxe/sij[/face] as interchangeable. Note that one use of the article with a predicate
substantive is to establish this identity with the subject. I'm not sure that the sense of this differs at all from the original sentence.