A couple of quick thoughts:
1. I'm not reflexively against passive skills. In some ways, passive skills can actually be more valuable than active skills -- if they're "always on," you don't have to pay to use them. That can add up to big savings over the long run. But of course you could also look at that as a reason to keep a tight lid on such skills when you're designing a game. (And that goes at least double or triple for a PvP game.)
Another aspect of this is that, given the numeric nature of RPGs of any kind, developers often find passive skills easier to implement. Because you don't have to show them being activated (often requiring art and audio assets to be created), you can just make up something that changes behind-the-scenes numbers and call it a passive skill. The result can be an awfully strong temptation to just crank out a passive skill when you're on a deadline and have to come up with something to round out a character ability set.
So I'm not anti-passive skill. I'm just cautioning against relying on them too much.
2. For NPC reactions based on a player's "skill level," I should have defined my terms better.
I'm using "skill level" here to mean the total number of skill points (or prestige points, or whatever) that a player has sunk into the skills of a particular branch (including Command).
This would reflect the ability of NPCs to look at a character and make a reasonable guess about what they do and how good they are at it. Unless they’re a Master Hacker who broke into the Starfleet Personnel database and inexplicably chose to spend their time there reading your dossier, there's no way the NPC would know that you've got the Plasma Conduit Scrubbing III skill -- but they might reasonably be able to peg you as an Experienced Engineer.
So what I was suggesting about NPC reactions wasn't about them seeing specific character skills. It was about them seeing a character's primary capability at a gross level, and modifying their reaction somewhat (not hugely) based on that observation.
And absolutely the reactions of NPCs should be improvable... unless you've somehow made yourself KOS to them.
But that should take conscious effort on your part.