I think this is actually a very good idea, more ‘organic’ (if I may make a pun given the context) method of creating the ‘special’ zombies than our current spawn ratios. (aside from technological or fungal variants of course)
Applying mutations over time could help ease up the early game a little while making any zombies that survive your initial purges potentially (they could get a really bad luck of the draw too) dangerous in the long run.
Spoilers Ahead:
Personally I’d suggest that the zombie mutation be based primarily on time, and possibly their extent to which they’ve managed to recover and concentrate the contagion The Goo/Netherium in their bodies through http://smf.cataclysmdda.com/index.php?topic=2099.0
Remember, the player can refine his own mutagen from tainted meat and I think if our Unfriendly Neighborhood Hyperspace Slime realized that it’s forces were getting fucked up in any significant numbers it would try and switch up the game a bit.
Then again we could always place this idea in the category of ‘humanoid mutants’ rather than proper ‘zombies’? Perhaps gibbering, ghoulish ‘survivors’ who refused to die and were driven mad from mutations as they survived on tainted flesh? Now I think, this apocalypse is rather up to it’s gills in zombies, we could probably use horrible mutants as a more varied and potentially challenging ‘second wave’.