I have mixed feelings about the Yiga Clan.
As with almost everything else about BotW, there is something about that discovery phase when you start the game and first start exploring the darkened map. I had lit up the West Necluda/Dueling Peaks area first upon leaving the Plateau, as I think that's the way the game first directs you to go to get to Kakariko. But somewhere along the line I think I ended up climbing a big mountain and flying or falling off of it into uncharted Lanayru territory. I came around a curve and there was some dude just standing in the middle of the grass and he was a little weird and suddenly he turned into this brutal red guy that reminded me a LOT in his fighting style of Ghirahim from Skyward Sword.
At that point in the game, there was something really thrilling about this stray enemy warrior who was much tougher than the bokoblins I'd mostly fought up to that point. He was scary and hinted at the promise of the game, which was still very new to me. And the bananas he left behind were quirky and baffling.
From that point on, I found the way the Yiga story plays out to be fairly satisfying. I enjoyed the sidequest from the Gerudo Town that makes you find their hideout and at the time of meeting Kohga it was kind of a relief to have a big bad be a buffoon. But after defeating Kohga, there was no more mystery to the Yiga Clan, and no more threat really, although it is AFTER you defeat Kohga that they start coming out in droves randomly no matter where you are, and they're all the same and just annoyances (and rarely as tough as they were in their own hideout). So that's the downside. It felt like a lot of promising build up but no second, additional level of threat or story after that initial Gerudo sidequest.
I think all they really needed was an extra level of toughness or a third type of warrior to appear after Kohga's defeat. I like that they're quirky and culty and silly, but also want them to be legitimately scary when they pop up out of nowhere.
Their weapons are rubbish, too. They all have cool names and menacing looks, but they break so easily...
P.S. I didn't complete the Dorian story in Kakariko until almost the very end of the game. I wonder if that might have affected or heightened the Yiga Clan story for me in some way.