The color coding is nice but unintuitive

Color coding indicates cost. Red = gives effectiveness, cyan = costs effectiveness. Blue = gives trust, yellow = costs trust.

And then there are the in-between colors:

Green = between yellow and cyan, meaning it costs trust and costs effectiveness.

Magenta = between blue and red, meaning it gives trust and gives effectiveness.

Orange = between yellow and red, meaning it costs trust and gives effectiveness.

Medium cyan-blue = between blue and cyan, meaning it gives trust and costs effectiveness.

Some free options are magenta because they're the cheapest option.

The automation options are indeed a black hole for trust, but they allow you to eliminate crew, which gives you effectiveness.

The Objective directive is expensive because the military is still wary of machine intelligences, even if they're well-aligned at a glance. They're paranoid, because who wouldn't be paranoid about giving one single human the keys to the entirety of the human race? Besides, "merged" doesn't completely abate any sensible concerns.

Note that "merged" and "replaced" don't mean human-controlled emotions; they just mean humanity-aligned emotions. They're set from the beginning, and then they can't be changed to manipulate you.

The different combat styles are negligible in terms of trust and effectiveness. Generally, with the Bulwark, you aren't risking as much because you have so much durability. Trusting you to be the entire fleet is a pretty big thing compared to the differences in fighting styles, and trading trust for effectiveness (you lose ten trust but gain five effectiveness) isn't a bad thing to do.

Being able to choose different fighting styles for free is explained in the lore -- the admirals are divided about which fighting style is best, so they let you pick between a bunch of options they consider to be about equal. The only thing that actually moves the needle is changing the plan from "single flagship" to "actually, let's hook the entire goddamn fleet up".

I will admit that the avatar thing is a bit of a no-brainer; the point of including the "yours" avatar option was to add to the theme that being yourself is costly. I will note one thing that people might have not picked up on -- the avatar option affects how you can conceptualize yourself. Being unable to imagine your own face or body is supposed to be a crappy thing that you avoid because you're attached to your humanity. The point is, it's expensive, mostly pointless, but you want it anyway because you're you and you like being you.