If you can't see the difference, then I'm sorry, but that's on you. It's a big obvious distinction psychologically, between a massive magical monster, and a single guy who could be a PC. The main difference, if you really can't see anything else is that players realize that they can't easily defeat a dragon, but with a single human, they are unlikely to realize that until after the fact. That means that each failed roll, each round you don't manage to stop him, is going to sting more, and it's going to vex them more. You think that's going to translate into fun. I very much doubt that. If you don't care whether it's fun - well, okay you're "that kind of DM" and yeah fine, then advice is immaterial and this discussion is over.
Maybe I am "that kind of DM"? I guess? I don't know. I don't consider the success/failure/fun/not fun of a campaign entirely on one encounter, no. Not ever single encounter/scenario/scene in a game has to directly translate into "fun" so long as overall the game experience is fun and satisfying for everyone involved.
If the encounter is designed to "hurt" in terms of PC failure, I don't care, no.
But I would rather the PC's interact with a scene rather than just cut scene. It is a shared narrative. I want to know WHAT the PC's try to do to stop something, I want to know HOW the PC's feel in that situation... as reflected by the players statements of actions and those feelings. I can't get those in a cut scene.
I would think that low-level PC's seeing someone running on the walls or ceiling with a glowing sword, might give them pause about their chances vs. that NPC. I certainly would if I were playing a level 1 PC and saw an assassin running on the walls, etc. have immediate doubts about my ability to fight them.
This goes double if you're giving him Advantage on rolls that he shouldn't necessarily have Advantage on (like if you wouldn't give a PC Advantage there, he definitely shouldn't get it!). He certainly wouldn't have Advantage against Command or Hold Person or the like either, which makes this very fragile and potentially likely to end up with him getting Command'd to the floor then wrestled by PCs whereupon, if he's many levels above them, he may just have to start one-shotting them, which isn't going to impress anyone.
I never said giving advantage on saves? I was just referencing back to the OP's encounter concept card that talked about advantage for the assassin or disadvantage for the PC's because of the unconventional nature of 3D combat that the assassin is trained to deal with while they are not. I probably would just do disadvantage on attacks if anything. But that isn't necessarily.... necessary. It's just part of the encounter card that I was again, referencing.
I haven't talked about "powerful NPCs". So that's a strawman. I've talked only specifically about overpowered-ninja-style NPCs. That is a different category to "powerful NPCs" (a highly specific subcategory if you will). That's what I'm trying to convey here. How many OP ninja-type NPCs have you used before? Or seen as a player?
It's not a strawman. I'm not talking about an "overpowered-ninja-style NPC", I'm talking about a NPC who is more powerful than the PCs. If you want to get nitty-gritty with it, I'm talking about a Hexblade Pact of the Blade Warlock with a few invocations and spells that let him walk on the walls/fly. Tht would have proficiency in Wisdom saves and so be more likely to NOT fail those saves vs. specific spells like Command or Hold Person, etc and who has spells at their disposal to get out of a grapple if necessary.
The card specifically says the assassin is after their target only and won't try to harm the PCs (Prologue Szeth, not later Szeth).
You literally counter your own statement here by calling your weirdly specific thing a "subcategory" of Powerful NPCs... so yeah.
I've never seen any before in a game, nor used any. That's why I think it would make for a memorable and fun arc for a game because I've personally never had it.
I've seen a wide variety of "powerful NPCs", some unbeatable, go up against PCs. Only two categories have universally provoked derision/disdain/annoyance. Higher-level NPC spellcasters who just CC the naughty word out of everyone all the time (nobody enjoys this) and NPC "overpowered ninja"-types, who tend to be like, obviously a ninja/monk, usually with some kind of wacky over-the-top weapon (which works in the Stormlight books because there are a whole bunch of them), and tend to show off by killing people in front of the PCs (this is not new trope - though wall-running of a literal kind is!). These guys don't go on the "We've got to kill this guy!" list of the players, because they're not fun to engage with. They go on the "Oh naughty word that guy jesus ugh let's hope we never meet him again" list of the players.
I'm not talking about a "Wacky over-the-top weapon" here? I'm literally talking about a Pact of the Blade warlock with their pact weapon... so yeah. I'm not sure why you keep bringing up this hypothetical NPC bad guy who is Szeth-
like as "overpowered" when you can literally build one from standard rules with the standard array.
More powerful than players? Sure for now. Overpowered, I don't think so.
Also, it's on the DM to work with the players and the story to have a compelling reason for PC's to do ANYTHING. This shouldn't be any different than your hypothetical Dragon encounter. Dragons' shouldn't naturally go on the "we've got to kill that guy!" list of the players' either, they should for any sane character go onthe "f that guy, jeez ugh, let's hope we never see that dragon again." list of the players'
What's particularly problematic as well is that these guys usually aren't going to be very possible to stop later on. Well-designed ninja types can, barring bad rolls, escape from pretty much anything forever. Nasty CC types are going to CC a bunch of PCs no matter what (concentration makes this less of an issue in 5E thank goodness).
I assume the rapid rise of PC's in abilities outstrips the NPCs.
So while this assassin took years to hone their craft and rise to the lofty power level they're at when the PC's first meet them. They are relatively static/plateaued in their growth, so by the time the PC's meet them again (end of the chapter/arc/whatever) they're now level appropriate. Maybe a hard encounter but level-appropriate now. If it's level-appropriate, then the PC's should be able to either kill or stop them from escaping through their very many more tricks that they have up their sleeve now: flight of their own, counterspell, etc. etc. etc.).
Re: good faith I'd say lay out what you're going to do here, how you're going to play it, and so on, and then do that, and then report back honestly.
I'm not DM'ing for my group right now, just playing, so it might be a while before I get a chance to do this, but I will do it when I'm up.
What I'm going to do is exactly what we talked about.
A 9th level Hexblade Pact of the Blade Warlock with their abilities walking on walls, etc. as an Assassin that the PC's have no warning about will appear and attempt to assassinate someone they are either friends with or paid to defend. They will likely succeed in that attempt and do their darndest to get away cleanly.
Players are creative so they might not getaway. it also depends on how many NPC guard types are around, etc as well as Action Economy, which far more so than anything else, is ever the foe of single NPC enemies