I assume you're getting some of this idea from Dolphin. There's two possible problems:
- Is it possible? I'm not too familar with the inner workings of the PICA200 GPU, so you'd have to ask a dev about this.
- Is it practical, and worth it? For this, I think it might just be a no. Dolphin massively improved shader compilation with Ubershaders, but Dolphin has very well optimization, and accuracy otherwise. The latter still isn't all there in Citra, so I feel that that should take priority over improving shader compile time.
That's another question that a dev could probably answer better than I could.