Yea, that whole league thing is messy in so many ways. I think it would require a bit of an overhaul, but we can dream.
Triple Threat stuff:
I like the "Just get rid of the regen tick if they drop below 5%." You'll still need to make sure your players don't screw it up, so still a challenge.
Awarding badges for completing phases sounds very reasonable. (In more that just Mag)
Mini-Tyrant stuff: yes. (Though I didn't know he existed anywhere before the shrinky dink bit)
Quill change sounds reasonable
And completely not thinking of a change, but "teleport arrow"?