And when I say "multidimensional", these folks can be seen in a positive light.

When I think of the word "multidimensional," I think of digging into the character's history and trying to understand them better. What is this character's background? What led them to think the way they think? What might have the character turned out as, if x hadn't happened? Is there anyone in their life who sees them in a good light, and if so, why? What is their relationship?

I always think it's important to carefully evaluate characters and try to walk in their shoes when possible. When we vilify a person, we lose sight of the humanity within them. Of course, this does not justify their actions nor does it make them a hero. But it does make us stop and think a minute about how a person's situation shapes them.

Question is, how do we see a good side in, let's say, the Mind Flayer?

The Mind Flayer is an interesting villain in that we don't actually know much about it. In that way, it's hard to go deeper when evaluating its character. That aside, though, I do admit that I was thinking more of human villains in my answer, as I find them much more interesting.

Nah, it will mess up the storyline even more.