Throughout the course of The Walking Dead's run, the core group of survivors has run into all manner of enemies. Some of them were minor menaces while others became existential threats, but the reality of this apocalyptic world that the survivors exist in is that there is always another danger lurking around the corner.
Every villain that The Walking Dead characters have come up against has ultimately been a fallible foe, but some of them were bigger, and more importantly more intelligent, threats than others.
Walkers
Ironically, the least intelligent villains in The Walking Dead are also the most consistent and biggest threat to everyone left in the world. The walkers are barely more than ambulatory potatoes, and nearly any living thing with a brain is more intelligent than them.
However, they're a scourge on the entire world, and the fact that every person becomes a walker when they die (unless their brain is damaged in some way) still makes them a serious danger.
The Wolves
The Wolves clearly had a few decent tricks up their sleeves, and the whole trucks-full-of-food gambit was clever and tempting enough that it almost got Daryl and Aaron killed.
However, while they were built up as a potentially significant threat, beyond their attack on Alexandria they didn't do much. Besides, the Alexandrians as a whole aren't known as the toughest bunch, so the fact that the Wolves were so easily felled by them doesn't make the group or their attack on Alexandria seem very clever.
The Whisperers
The Whisperers seem to at least have some good strategic ideas that they employ against their enemies sometimes, and their ability to corral the walkers and use them as the ultimate zombie weapon is impressive, but overall they don't seem to have a lot of good ideas beyond that.
Their whole ideology is one that doesn't seem to work well in the long term, and it seems like Alpha was the only real driving force behind them.
Beta
Although Beta was the second in command presiding over the entire Whisperers squad, he was honestly barely more intelligent than the people that he was leading. Beta was a bit savvier than he sometimes let on, and he wasn't easily fooled by someone like Negan.
However, he also had no independent thoughts or ideas to speak of, and he seemed to want nothing more out of life than to serve Alpha, remaining loyal to her even after she was dead.
The Terminus Cannibals
Regardless of how horrifying it is, it's hard to deny that at the very least the whole Terminus scam was a relatively clever one. Presenting themselves as a sanctuary for all was clearly a good strategy for getting hundreds of people to come to them, and while it's disgusting, they did essentially design the easiest food self-delivery system imaginable.
However, the fact that Carol could single-handedly destroy them, and the fact that they don't even bother checking their food for walker bites apparently, makes them seem a little stupid.
Gregory
Gregory may be one of the most cowardly survivors in the history of The Walking Dead, but he does have a certain kind of cunning that kept him alive much longer than he should have been, and he managed to make a significant number of political plays and manipulations based on his intellect alone.
Gregory had no survival skills outside of his ability to suck up to the right people and to manipulate everyone around him, but the very fact that he could read other people so easily indicates a certain level of intelligence.
Alpha
In order to lead so many people, obviously someone like Alpha would have to be relatively intelligent. However, her ideology about the way the world is now as well as her incredibly brutal leadership style seemed to be bound for failure at some point, as it's a very hard way of life to sell to anyone who has lived in the real world.
And of course, her confidence in herself and her own power was her ultimate downfall, which is something that anyone with a shred of introspective abilities would have seen coming.
Shane Walsh
Regardless of the fact that Shane became more brutal and unpredictable as time went on, it's hard to deny that his ability to adapt to the new world and become an effective leader was impressive.
And, although his mask did slip on occasion, what makes Shane such a dangerous villain is that he was much better than most villains at pretending that he wasn't actually a villain. Had Rick been a tad more ignorant, Shane likely would have won out and become the leader of the group.
Negan
Of all of the villains who have managed to build up a group that follows them, none has been more powerful or done a better job of building up that following than Negan has. That alone makes Negan one of the most intelligent villains in the history of the series.
However, Negan's fatal flaw seems to be his lack of emotional intelligence, as his cruel leadership style was clearly going to end up with many of those under him rebelling against him at some point.
The Governor
Out of all of The Walking Dead's antagonists thus far, there really isn't anyone who has been more intellectually well-rounded than The Governor.
What made Philip so dangerous is that he was very talented at appearing in the right way to the right people, for instance, he knew that he needed to be one version of himself in front of Andrea, but an entirely different person with Merle. He also figured out how to control people with kindness, which sets him apart from nearly every other villain on TWD.