The idea of using SMGs to proc Commando for free 9mm AR burst is good. Muzzled 9mm Chimera with Green Scope is the way to go, imo. Good for Aimed Shots, as well.
You could fit Snipe in there somewhere and use it to take down key targets, retreating with Vanishing Powder Grenade after so you can switch to your AR.
Since you're going Rathound Regalia you could just lvl enough Biology to make Focus Stims and enough Chemistry to make MKIV Frags. No need for Three-Pointer; that feat is taken with max-Dex-max-Throwing. Don't say they are useless, though
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You could swap Trigger Happy for Quick Tinkering. You have loads of Stealth so you can always scout enemy positions and spot the stealthed ones before they spot you. Basically starting combat on your terms.
You might want to skip later arena fights since you won't be able to start combat deterministically.