Pun-Pun is an amusing exercise in rules lawyering, but a gentleman doesn't bring such a monstrosity to the gaming table (on either side of the screen).
While there is a vast optimization difference between Pun-Pun and a wizard who thinks magic missile is a great spell, most characters tend more toward the lower end of that scale. Not everyone is going to dish out the damage of a Mailman or Hulking Hurler, or force seven saving throws per round, or even pull off a dimension door pounce.
The issue you'll run into is that some characters will utterly destroy any halfway reasonable encounters you throw at them, forcing you to use unreasonable encounters that will overwhelm the non-powergamers. This, and the silliness that some of the more "broken" builds do (throwing a 13 ft. diameter +1 returning ghost touch etc. lead sphere as an improvised weapon for over 1,000 d6 + Str mod), will make it hard to weave a logical story and keep everyone involved.
If it's just a murder simulator with no story, it'll work just fine.