Regarding Paris' reinstatement...
I just rewatched the dialogue from "UNIMATRIX ZERO' to be certain, and it is clear. Janeway said 'reinstate', not promote. Which means Tuvok was the only person who ever received a promotion. Everyone else received field commissions (Torres, the Maquis crew) or had their ranks reinstated (Chakotay, Tom).
Which is what Janeway thought, until she realized that B'Elanna was the more talented engineer. And if one is going to complain about B'Elanna becoming Chief Engineer, why not complain about Tom becoming the Chief Helmsman? You mean to say that he was the highest-ranking pilot aboard Voyager at the rank of lieutenant junior-grade and later ensign? Why not complain about Harry being the ship's Operation Officer and a member of the command staff, despite being an ensign fresh from the Academy?
I'm still complaining about Montgomery Scott being the Enterprise's third officer, despite the fact that he was not a Bridge officer. Sulu should have been Kirk's third officer. The Trek franchise tried to cover its ass with this mistake by allowing Charles "Trip" Tucker to be the original Enterprise's third officer, despite him not being a Bridge officer. Reed should have been Archer's third officer. The Chief Engineer might be part of the Command staff, but he or she is not a Bridge officer. Which means, he or she has no business being in command of a starship, unless all of the Bridge officers are disposed or unavailable.
It makes sense that Trip was third in line for command on ENT. First, he was a full commander, so he outranked everyone except Archer... and later T'Pol, when she got her Starfleet commission. Second, considering his extensive knowledge of the warp 5 engine, he was very well suited on kniwing all the capabilities of the
Enterprise when an emergency occurs, making it easier to come up with solutions to emergencies quickly. Third, he had been in Starfleet for a long time, and had a great deal of experience, especially compared to Reed. And fourth, Scotty was seen in command on multiple occasions in TOS.
In TOS, Scotty was also outranked on the
Enterprise only by Kirk and Spock. He also knew the ship extremely well, and he had been in Starfleet for a long time and served on multiple ships prior to the
Enterprise.
Sulu was also in command multiple times, and both he and Scotty did their jobs well when in command. I have never had a problem with either being in the center seat when called for. (Particularly Scotty, though we had seen more scenarios where he could shine than Sulu.)
Tucker was not always level headed when he was in command, but he did more good decisions than bad.
Regarding the VGR examples...
As far as we know, Paris was the highest ranking helmsman on board... at least, before he got demoted.
And it is puzzling that Kim would be the head of Operations when we have seen other lieutenants on board, like Durst or Rollins. So I have no idea about that one.
And as for Torres, it makes sense (at least in the first couple seasons) that she would never be in line for commanding the bridge because she never graduated Starfleet Academy.