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Suffice to say that the interpretation of the Prime Directive is a big issue in and/or with Star Trek. There's a very clearly defined principle that is 'the spirit of the law.' But in practice, actual Starfleet officers seem to whipsaw back and forth between Lawful Stupid behavior and "be humane" behavior and "fuck y'all, I'm angry" behavior and coming up with weird justifications.
Military regulations should be crafted to a higher standard than that. Among other things... what you're saying, that if Janeway never violated the Prime Directive she is unfit for command? Yeah, that may be true, but if it's true then the Prime Directive is incredibly poorly written, and/or the Federation hasn't put nearly enough effort into organizing the case law on the subject into clear guidelines for its own captains.
It's a partial explanation, but it's not like regular Starfleet captains never have problems serious enough to present quandaries and difficulties. They should still be good at what they do.
It also illustrates a fundamental problem that the Explorer Corps is likely to create for Starfleet: when you take the top 20% or so of your recruits and put them in an elite sub-organization, by definition it means that almost nobody in the regular fleet is in that top 20%. This is especially problematic since Explorer Corps crews do almost the same things as regular Starfleet ships, just more intensively and under slightly more difficult conditions.
The only remedy I can see is to make sure that Explorer Corps personnel are constantly being shuffled in and out of the regular fleet. And to be fair, given that we only really see what goes on at the 'captain' level, that seems to be the case. Let's see...
Mrr'shan at least had a brief stint aboard a regular escort. Straak served in the Explorer Corps as a staff officer but before THAT he commanded a Constellation. Mbeki, likewise, commanded a Constellation for five years before being appointed to Explorer Corps command (as did Thuir before him). McAdams commanded a regular fleet Excelsior for a few years. Going back to former Explorer Corps captains... actually I have no idea what Eaton and T'Lorel were doing before 2301, though we know Nash commanded a Miranda.
The worst 'offenders' in this respect are probably:
1) Maryam Ajam, whose only non-Explorer Corps service in the past ten years or more* was in the Cardassian navy! And, lo and behold, we're giving her a command that is so Explorer Corps it's got a crunchy Explorer Corps outer shell wrapped around delicious Explorer Corps filling with extra Explorer Corps sprinkles on the top. And...
2) Saavik, who is a strong candidate for 'career Explorer Corps' since she was Straak's XO prior to receiving command of S'harien. Note that when she was first seen on Enterprise, Enterprise was a training ship, though- not a frontline explorer. So maybe she served her time in the regular fleet in the 2290s, and even up past 2300 since we don't know where she served from 2300-2305. If she'd been under T'Lorel I would think someone would have mentioned it. And of course...
3) Then there's Nash, who is Explorer Corps from the tips of her antennae down to her toenails (I assume Andorians have toenails)- but who is also exactly the sort of person the regular fleet needs just as much as the Explorer Corps, because her gift for getting the best out of her people is at least as useful when you're not already commanding a handpicked elite.
Anyway, the real question is, to what extent does the Explorer Corps remove a certain vital spark from Starfleet by taking it out of the rest of the fleet to concentrate it on the explorers, versus to what extent does the Explorer Corps inspire the rest of the fleet and ignite it by taking personnel who've served aboard its ships, and parceling them out among the rest of the fleet to spread the awesomeness?
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*I don't remember if she was on Lion with Nash back in the day
Ajam was Excelsior when it was EC then over to regular ground postings groundside before assignment to Enterprise. Most EC officers have spent time in the regular fleet. Zhang was regular fleet up until going to Enterprise, Taggart was EC then over to Sappho which was regular fleet.
There seems to be a thing where the EC starts to bottleneck after Lieutenant so that they feed back out into the regular fleet for promotion then a few of them get fed back in to be Captains. I honestly can't think of a single officer that's never spent time in the normal fleet.
I don't think the EC/Regular fleet distinction is actually that much of a thing, because narratively it /never comes up/ as a thing. It's never shown as a hard split. People go back and forth.