I previously mentioned that I would like additional officer positions, because I was coming at that argument from an immersion & consistency perspective. Consistency being a uniform "captain applies half bonus, specialist provides full bonus" across all commander bonuses. Immersion being that more positions leads to more varied & detailed careers for officer characters.
That said, I can appreciate how the gameplay effects, and decision-making qualities, mean that some things would always be used, because there are few reasons not to.
Plus, since not every officer rank is explicitly modelled, many positions would be held by junior officers, below the game's level of abstraction.
i.e. the lowest rank for naval officers is Lieutenant-Commander. A cargo ship might conceivably have a loadmaster, but that might only be a role for a Lieutenant, which would be one of the unnamed "junior officers" ingame. And even on a large cargo ship, is the loadmaster a senior enough position that it would be a billet for a Lt.Cmdr ?
That said, I think there are a couple slots where there is room for meaningful decisions.
The Diplomacy module, to make a ship a diplomatic one, is 500t, and means the ship requires a Captain, rather than Cmdr or Lt.Cmdr.
With this required rank increase, there's a possibility I feel, to appoint a xenolinguist to the diplomatic ship, to provide a bonus to diplomatic effectiveness and/or efforts at translation.
So a diplomatic ship would have two officers - the Captain (using their Diplomacy bonus), and the Xenolinguist (using their Communications? bonus [I'm not entirely sure what the Communications bonus actually does])
There might even be a case to have a dedicated Ambassador, (using their diplomacy bonus), with an even larger "Embassy" module. (10x the size of the DIP module maybe).
Since pure diplomatic ships are fairly small (even my jump-capable ones are only 5000t), then there's a bit more of a decision on whether or not to include modules that would increase their size.
The ELINT module is another one where I think there might be a meaningful decision to be made.
One of the ships that I was using in my game, was a cruiser which had an ELINT module on it. It wasn't the ships main role, it was a frontline warship that also happened to be capable of gathering ELINT.
Now then, with ELINT modules coming in at 500t, then... another module with an intelligence analyst officer might be a meaningful decision to make.
It'd be a straightforward decision to put one of those on a dedicated intelligence gathering ship, which would carry multiple ELINT modules anyway.
But on ships like my cruisers... do I want to spend a couple hundred tons to make it slightly better at ELINT whilst still being a standard combatant ship ? Do I want to use that tonnage on another CIWS instead ?