Samus's status as a bounty hunter is only relevant in Other M insofar as she uses it to comfort people who are scared of the Galactic Federation. She was not hired to investigate the Bottle Ship, she stumbled upon a GF operation and invited herself into it, because her gut told her that they were about to get in over their heads.
I think it's funny that everyone complains about Samus allegedly having no will of her own when working under Adam, when in fact Adam did not want her in the operation in the first place. There is a lot of selective reasoning going on in Other M's criticisms.
My beef with Other M was the "authorisation" thing as a whole.
Samus, the independant bounty hunter, refuses to activate features that would help her in her mission until she gets the say-so from a man who has no direct authority over her? I get the whole "issues" thing, but really?
What Fusion told us: Samus took orders from Adam and trusts him, but dislikes taking orders in general.
Your complaint is a common one, but it's also ignorant of the game's presentation. Do you know how many upgrades Samus de-activated when she decided to work for Adam? Two: Bombs and Missiles. She, of her own accord, turned everything else off before she knew Adam was anywhere near the Bottle Ship. She also activates her gear at her own discretion (being rather snarky about it, I might add) when communication is cut off, AND she activates any new gear that she finds (Diffusion Beam and Seeker Missiles) immediately regardless of her communication status.
I see this as an X5 "don't get lazy and depend on the power of the armor" situation. Same reason the escape sequence is played in the Zero Suit. Samus is not just her suit, she is a Chozo-trained super-athlete who continuously keeps herself on her toes. And with how often her gear gets stolen, disabled, or damaged, it's not as if she doesn't have good reason to.
I thought one of the main problems is that there are few/no charitable interpretations of most of Adam's actions towards Samus. Like, does the game even try to explain why he waited until Samus was on the verge of death-by-heatstroke to authorize use of her Varia suit? It makes him come across as callous, or that he foolishly overestimated Samus's endurance, at best.
The charitable interpretation is that Samus was pushing her luck; Adam did not direct her to that battle. A big part of Other M's premise that everyone overlooks is that your primary mission is not to kill things, but to search for survivors, so the less hospitable an area is the less reason Samus should be there to begin with. If you wanted to stretch it you could also say that there is strategic value to holding off on the Varia's activation since it comes with a full health restore.
I will admit that needing authorization for a purely defensive function is silly, as is splitting hairs between the GF Trooper's freeze guns and Samus's Ice Beam, but I see that as Adam running a tight ship, not an issue between Adam and Samus specifically. Adam does care for Samus but he is an overall cold/ruthless character. Again, well in line with what Fusion told us.
That, and from what I understand, the presentation of Samus's vulnerable side didn't feel natural/wasn't handled well, what have you. I would have at least made it a bit more subtle.
Most of the people who make that criticism don't want her to have a vulnerable side to begin with. The dialogue is a little heavy, but it works a hell of a lot better than anything concerning Melissa.
You know what I liked? The flashbacks about Adam's brother, when Samus was talking with Anthony. Nobody really talks about that, but to me it was the best illustration of how Samus "grew up" after leaving the Galactic Federation. She stuck to her ideals where others would have become more jaded with age, but she also learned to respect people who don't agree with her.