(And can I have a big "WHAT A HECK BLOGGER?!" I've changed the timestamp, but it's giving an even weirder post time than before... [Er, nevermind, I didn't have the right timestamp, but it's still way wrong, more so than it should be.])
This post is another greatly overdue one, originally "forecasted" here. It's recommended that that post be read before this one.
Many of the later Brave Robots series dropped the earlier conceit of the villains being similar to the heroes. While I can't speak for all of them (Brave footage and information is always kind of scarce), I do know that some of the series, such as Dagwon, had at least some enemies that were monsters instead of robots. (I think that thing's a monster, anyway. Could be wrong.)
The series for which I can speak most confidently is GaoGaiGar.
GaoGaiGar, in a post-Evangelion anime world, had to raise the bar. Its enemies couldn't really afford to be simplistic, weak enemies. GaoGaiGar's first major enemies were the Zonders.
While mechanical in basic nature, the Zonders upped the villainous ante by having durability far in excess of believable limits, as demonstrated by this video.
As this video also demonstrates, while they are tougher than nails, the Zonders are also considerably dumber than nails. (I mean, look at him just sit there after he finishes regenerating.)
Another characteristic of the Zonders, related to the regeneration, is their ability to reshape themselves completely to their own will. Since Zonders are dumb as rocks, they only usually use this ability effectively when being managed by one of the "Four Machine Kings" early on. (Later Zonders occasionally show signs of intellect.)
Zonders' forms are heavily determined by the fact that their bodies are built by absorbing machinery. (Zonders are actually not true mecha but humans who have been transformed into quasinanotechnological lifeforms by exposure to a substance called "Zonder metal." They are also powered by stress. No joke. Since they are restored to normal after the Zonder's defeat, the individual is always grateful, because they've had all their stress removed in the "purification" process. Again, no joke.) Sometimes this mostly means that their weapons are derived from what the Zonder uses to build its body, as with this one.
(Also note this Zonder's rather strong resemblance to a Zaku. There was also a Zonder which originally merged with a train and later with a space shuttle, a somewhat oblique reference to Astrotrain, and a Zonder which could have been a baby V'Ger. I suspect that many of the other Zonders were also paying homage to other pop culture stuff.)
There are also much more extreme instances of Zonders resembling what they absorb, such as this Zonder, which absorbed a big old railroad cannon.
Note GaoGaiGar's creative usage of his space-warping weapon there. He increased the distance between himself and the incoming shell.
After the Zonders were defeated altogether, the Primevals, which were basically smarter, stronger Zonders, showed up. They all had body part themes. (I'm not touching that one.) This eventually led up to them being parts of a larger entity.
In the GaoGaiGar OVA, FINAL, the series ironically reverted to relatively more traditional piloted mecha-like enemies, although for the most part they still did most of the same stuff Zonders did other than absorb things.
-Signing off. Also, the first half of this blog took fifteen minutes, the next fourth took an hour, the eighth after that took TWO FREAKING HOURS, and the last three paragraphs, where I finally moved to a new window, took five more minutes. Stupid computer.