Max-imum agents
I would definitely handle it as a Department. The question is one of power level. Do you want the chimera to have enough of an advantage over "regular" superspies that a ECL is involved? If not, I would look at probably a +2 to Strength and Dex, and a -4 to Cha (sure, she's pretty, but abrasive as hell and not totally socialized), department bonus to spot and listen checks. department bonus to reflex saves. Rather than a feat maybe 90' low light vision and the equivalent of the scent feat.
The rest of what we see from Max I would consider a function of her training in the program and later experience (i.e. levels). Level or three in soldier, ditto in fixer and you could be in business. Eye towards high Strength during creation and posible martial arts feats during career.
If ECL doesn't present a problem, you cold go hog wild, but in practice the vitality you lose to ECL in a party of the same level gets crippling up above ECL +2...