Counterspells in MTG are a **** good example
I was on board up until this one line.
I want to preface my response by saying that I don't generally play counterspells myself, just so you understand which end of the argument I'm coming from...
Counterspells in mtg are one of the worst examples of an npe that could ever be chosen.
Sure they're frustrating for someone who doesn't know how to deal with them (quite a few things in x-wing fall under this banner), but once you know what you are doing they deepen the game so much.
Some of the tightest, most interactive and tensest games of mtg that I have played have been against people with counterspells.
They're misunderstood, maligned even... But the only npe they cause is that people don't want to put in the effort to work around them.
To bring this post back on track to x-wing; I see a lot of things banded around as npe's and for the vast majority it's things that can be played around. It makes me kinda sad that people would rather just remove these things instead of learning to defeat them.

