I think you kinda have to strike a balance. For instance, Mario is my favorite series and I've 100%'d pretty much all of them numerous times, but I will never, ever bother with Sunshine, and I even liked the game. The blue coins are just garbage, and even though I certainly could do it, the act of getting them isn't fun or rewarding, and neither is the end goal (just changing the picture at the end of the game? Yikes). But I did beat all the levels with all five characters in 3D World to get those last stamps because I enjoyed the game so much I didn't want it to end. I guess what I'm saying is, as long as a part of you is still enjoying the game, even if it's some sad masochistic part of you, it's not time completely wasted.
I do think it's funny that so many people are bringing up the FFXHD trophy since that was the first game I actually got a plat in. Parts of it were brutal for sure, but it was mostly just an insane amount of grinding at the end, and I had a couple weeks of free time, so I just plowed through it on Vita while doing other things. Also while drinking. Lots and lots of drinking.