I've been building a melee character in preparation for trying the mutant questline, but didn't find much info available on what will actually help, so I did some testing myself.
First of all, as the wiki notes, upon transformation your stats will be set to 20 str, 7 dex, 3 agi, 12 con, 3 per, 5 will, 2 int. You'll be immune to acid and biological damage, but otherwise have no resistances or threshold whatsoever (unless you have conditioning). You will have no gear AT ALL: no shield, no combat utilities, no traps (TNT still works), no lockpicks; just your two melee weapons and your mutant body, which has 50% armour penalty (35% with nimble). As far as I can tell, any melee feats requiring specific weapons will not work, but more generic melee ones will. So no crippling strike, no heavy punch, no pummel, no combo, etc. However, things like dirty kick, expose weakness, and bone breaker work fine (bone breaker appears to fire on both weapons). Dodge and evasion still work, as does stealth, but with 3 agility, the armour penalty, and no stealth-enhancing items, you'll need a significant investment and probably interloper to be able to do much sneaking. Food still work as normal.
If there's anything I've missed, let me know and I'll go test it.
Edit: I've completed the quest, and would definitely recommend getting sprint, thick skull, interloper (with a lot of stealth), dirty kick, and yell. It'll make getting to the initial mutant starting area much more doable, since you have to pass through a few heavily-populated and entirely hostile areas. It's fairly straightforward after that. Thick skull could be picked up after turning into a mutant if you don't have enough constitution initially. The rest of your perks can just be whatever helps your character progress as normal, though as stated, melee perks not based around specific weapons will help.