As Sarta said, a lot of the problem with Kingmaker isn't the individual encounters, it's that it's the only one for the day, and the PCs know it. Also, if you do add many random encounters, the party levels so fast, that they walk through a lot of the Published content way too easily. I am continually having to amp up fights to compensate, and it becomes a perpetual issue of the Party (on medium advancement) out pacing the modules.
Editing was also a huge issue, especially in the first book. The 2nd wasn't much better. Stat blocks and creature powers and tactics were lacking or wrong.
Overall, I feel like the enemies are not diverse enough, especially through the first two APs. It's very, very melee/fort save heavy and most enemy casters only have illusions. I'd like to see more battlefield control tactics written in. And not as much opportunity for the PCs to isolate enemies.
Thorn Ford was almost a great encounter. Some traps and a little more ideas for tactics probably would help.
Make sure the Stag Lord has a couple of backup bows. Trust me. Invisibly, on a rogue, means his bow gets stollen.
The fey tower was a great encounter, maybe a bit more info to tie all the creatures together.
The Troll Lair was easy. Way easy. Needs some casters or something besides just big pin cushion/sparing dummies that the trolls ended up being.
The town of Varnhold could be buffed up a bit.
In Vordakai's lair, the occuus shrine, where if the PCs destroy it he comes... smart PCs make short work of him if they haven't gone through all of his minions. Also, the undead wizard was an under performer. Give him a wand of damage or something.
I highly recommend Vordakai have Silent spell or silent spell rod, or something. A lich in silence, in a corner, is dead meat.
I think that was the biggest issue. The AP feels like it's for beginners. Veteran players walk through a lot of these challenges from just knowing the system.
I use APs because I don't have time to invent the whole thing. If I have to rebuild every encounter, I might as well homebrew.