There should be a specific costume slot (given to all characters, in addition to their normal costumes) for EVA Suits. The options would range from all the different EVA suits that character has acquired (including the STF costumes). The options would work like how the STF costumes work now: Each costume would be selected from a drop down menu (Pre-Owned EVA Suit, Orange EVA Suit, MACO, etc). Things that can be customized (Like the STF costumes) would have those options, and other suits that aren't customizable (like the Current EVA suits) would have customization options grayed/locked out.
When you activate the power that puts you into EVA mode, it uses the costume data from this slot. Furthermore, the STF armor pieces (or the whole set as another 3 set bonus if the Devs prefer) should also include the 2 EVA suit powers, because it sucks to ruin the 3 set bonuses since you need to switch drop the STF armor piece. Boffs equipped in STF gear would use the default look of the specific set they have on.