If all you're going off of is the color palette, and if you're western-centric, then sure the original design seems "malicious". But that's just because it's big and black, and very naive mindsets just perceive that as "evil". The helmets looked more like giant bug faces than they did "evil" or "malicious", and if they were bright silver like the original T-51b's, then we'd think very little of the Enclave when we see them. But they were given a distinct look, and on top of which, distinct color palette, so they stood out prominently from any other entity encountered in the game, and it worked perfectly. Sentiments that the design catered to feeling exaggeratedly evil were merely simplistic sentiments to begin with.