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EddyBearr
I disagree with some of your assessments.
For starters, the presentation you chose isn't indicative as to the extent of losses/wins.
Going off the information you presented, I imagine you believe their MUs spreads would look like this (to reiterate, these MUs are not my personal belief, I am just speculating as to your opinion):
Samus:
Fox: Even
Falco: Soft Counter (Samus's Favor)
Sheik: Hard Counter (Sheik's Favor)
Marth: Counter (Marth's Favor)
Puff: Counter (Puff's Favor)
Peach: Counter (Peach's Favor)
Falcon: Counter (Falcon's Favor)
ICs: Hard Counter (Samus's Favor)
Doc:
Fox: Soft Counter (Fox's Favor)
Falco: Soft Counter (Falco's Favor)
Sheik: Soft Counter (Sheik's Favor)
Marth: Hard Counter (Marth's Favor)
Puff: Even
Peach: Soft Counter (Peach's Favor)
Falcon: Counter (Falcon's Favor)
ICs: Counters (Doc's Favor)
If this is the case, Doc's less polarized MUs would appear more desirable. Even if Samus does better vs. the three most popular characters in the game (which is debatable), there is no denying that her comparative superiority is marginal. On top of that, Sheik and Peach aren't far behind in terms of popularity and most likely overtake Marth if their communities were combined. As a result, her losses against Sheik/Peach are more significant than her marginal superiority vs. Marth.
Another way of looking at it is like this: There is a decent chance that Samus will have it marginally easier than Doc, but there is just as good of a chance she'll have it noticeably harder.
Of course, this is going by your logic. I personally believe that Doc does better than Samus vs. Fox and Falcon as well. He has a better punish game vs. both of these characters thanks to his CGs, tech chases, guaranteed high % fair, gimps, and polarizing stages such as FD (a stage which greatly works against Samus in the Fox MU). Doc is also generally harder for these characters to exploit. Fox won't be able to shark him in the air or kill him vertically as easily and Falcon, despite his superior range, won't be able to open Doc up as quickly (thanks to his smaller size).
>Hard Counters
Perhaps even more important is debating who has the more significant hard counter: Sheik > Samus or Marth > Doc. While you stated that Samus's comparative loss is lesser, this is simply not true.
To begin with, Doc does better against Samus's hard counter than she does vs his. Doc has a guaranteed 60+% chain grab against Sheik (which later includes countless follow ups and even a guaranteed fair kill at ~100%), legit gimps, and better neutral game options (like actual air mobility/cross ups and a jab that can lead to something better than ftilt). In contrast, Samus is totally outranged and outmaneuvered by Marth (advantages which she typically enjoys), has zero answers to a correctly applied Marth dtilt, and has zero advantages in the punish game unless you count attrition (which is another way of saying the Marth has to be worse than the Samus in just about every facet of their gameplay).
I bring up their respective counters first because it further demonstrates the extent to which they become outclassed in their actual hard counters. Much like Samus/Marth, Doc vs. Marth is incredibly ones sided in terms of range and mobility. However, Doc actually has a decent punish game vs. Marth. He has throw follow ups, can set up edge guards with space creating moves like dsmash, and has potentially good gimps. Samus, on the other hand, enjoys just as little advantages as she had vs. Marth as she did vs. Sheik, but with even
more polarization in regards to the punish/neutral game (I believe it was at BH4 where Mango said that no Sheik should lose to Samus at high level)