I ditched the idea of doing mockups using scripting from Photoshop. The primary reason was that Photoshops scripting capabilities are not great for doing WYSIWYG, i.e. every time a code change is made one has to reopen and reload the script. I had personally hoped for the ability to do F5 refresh of the script without any hassle.
Alas this is not possible. In any case, I actually did manage to produce a Mockup of a Red Alert inspired game using both real-time and turn based mechanics. This mockup was made using Photoshop and conventional tools.
I got heavily inspired by the graphics of the Cmd & Kill game made by renderhjs. Primary inspiration thread can be found at: http://polycount.com/discussion/120427/pixel-art/p10
I got the idea of combining RTS and Turned-based strategy. The concept uses two phases: planning & execution. In the planning phase, one plans troop movements, production etc. In the execution phase, troops move and attack. I made a GIF showcasing the concept.
I haven’t really decided yet if I want to pursue this any further - but I believe it can be made to work. Frozen Synapse uses something similar, although this is on a more tactical level compared to what I was thinking.