The first part of your rational only makes sense if you forget that the player can deliberately mutate himself, which is usually what happens, and its then the malmutators job to mess up your mutation set, which covers the second half of your rational.
http://crawl.akrasiac.org/rawdata/Dynas ... 162542.txt88532 | Pan | Gained mutation: You have an increased reservoir of magic (+10% MP). [a neqoxec]
88663 | Pan | Noticed Acidburn6's ghost (legendary GrFi)
88684 | Pan | Killed Acidburn6's ghost
88689 | Pan | Noticed Froll the pandemonium lord
88706 | Pan | Killed Froll the pandemonium lord
88756 | Pan | Got a demonic rune of Zot
88975 | Pan | Noticed Jemoney the pandemonium lord
88981 | Pan | Received a gift from Okawaru
88988 | Pan | Killed Jemoney the pandemonium lord
89209 | Pan | Found an exit through the horrors of the Abyss.
89279 | Pan | Noticed Shyplyxt the pandemonium lord
89292 | Pan | Killed Shyplyxt the pandemonium lord
89506 | Pan | Noticed Dooppas the pandemonium lord
89525 | Pan | Killed Dooppas the pandemonium lord
89699 | Pan | Found an exit through the horrors of the Abyss.
90235 | Pan | Noticed Klaepi the pandemonium lord
90240 | Pan | Killed Klaepi the pandemonium lord
90461 | Pan | Noticed Faomuol the pandemonium lord
90468 | Pan | Received a gift from Okawaru
90636 | Pan | Noticed Qeileplu the pandemonium lord
90649 | Pan | Killed Qeileplu the pandemonium lord
90773 | Pan | Found an exit through the horrors of the Abyss.
91014 | Pan | Noticed Biugiag the pandemonium lord
91027 | Pan | Killed Biugiag the pandemonium lord
91296 | Pan | Found an exit through the horrors of the Abyss.
91311 | Pan | Noticed Premore the pandemonium lord
91321 | Pan | Killed Premore the pandemonium lord
91797 | Pan | Received a gift from Okawaru
91899 | Pan | Gained mutation: You are robust (+10% HP). [a neqoxec]
91960 | Pan | Noticed Stosoyri the pandemonium lord
91975 | Pan | Killed Stosoyri the pandemonium lord
91987 | Pan | Got a pair of ichor-stained gloves {god gift}
92120 | Pan | Identified the +0 pair of gloves of the Peculiar Demons {Str-4} (Okawaru gifted it to you in Pandemonium)
92156 | Pan | Gained mutation: You are partially covered in icy blue scales (AC +1). [a neqoxec]
Making it so that you can get more good muts instead of bad is not interesting, its amusing that you may end up with a good mut instead of bad because its rare. The rarity of mutations is what makes them interesting, not their effects alone. In the case you really consider mutations that interesting you can always play Xom or try Jiyva.