Thanks for the detailed review! Lots of good notes and areas of improvement.
Ah, very poor choice of phrasing on my part. I intended to suggest that the first level (i.e. only paper/scissor/rock) is well balanced (0'th prestige?) -- not the Well prestige. There is a deep well of issues with the Wells prestige. Sorry for being misleading there. I'm aiming to cover both prestige 1&2 with full upgrades and completion in the next release. Stay tuned!
I'm working on a fix for the blocking selection issue. In most of my balancing tests, I had completed the game option upgrades well before reaching rock never loses which often won't be the case. I also didn't want custom selection once you unlock Rock Never Loses for obvious reasons, but there are some other side problems created from that. I'm going to see how I can work around this. Good call out!
The mulligan issue is a major issue that I can't seem to root cause. Let me know if you notice any patterns for this.