Alright. I have three sort of major villains in mind, and three very different motives. First up, we have Giratina (if you're reading my fic and decided to open this up anyways, I hope you're happy that you've blown the surprise for yourself). Giratina's easy, as he wants to basically merge his realm with the "normal" world, effectively tainting everything with evil. This in turn causes everyone in the normal world to live in fear. Giratina then literally harvests that fear to sustain himself and grow in power, allowing him to become stronger and create "Fears" (may change to something less obvious and cheesy), which are dark copies of the creatures he harvests fear from. All of this is done to take power from Arceus, who had attempted to seal him away forever in an indestructible crystal using his own body.
Now for some harder villains. The first one I will describe is the more difficult one to create a motive for. Enter Darkrai, who is in fact a man in the beginning. He is part of the Elite Four (who guard and advise the king in my fic, as it's medieval times). At first, the reader thinks he is good, although they are perturbed by the name. Darkrai helps Latios and Latias find the Eon Chronicles, which they need to unlock a power to counteract a growing evil. The ironic thing is, the Latis do not know who or what this evil is for almost the entirety of the book, until it turns out to be Darkrai himself. The reader learns that he has been tainted by Giratina (who is still sealed in the crystal at this point, but can speak to people's minds). The reader also learns that it was Darkrai who taught Latios from the Eon Chronicles (which has to be done before a Lati can hatch in my fic). Therefore, Latios is also inderectly tainted by Giratina, and therefore falls under Darkrai's control. This leads to Darkrai gaining access to the Soul Dew (the hidden power), which allows him to create a sword that can cut through literally anything (this includes air, spirit, and lots more insubstantial stuff as well as physical things). With this sword, Darkrai frees Giratina and sets the union of the dark and light worlds into motion. However, since he has used the Soul Dew for evil, it consumes him and he becomes the actual pokemon Darkrai. *Whew*
So with that out of the way, does anyone have suggestions as to why Darkrai does what he does? I was thinking of just having him be under Giratina's control, and make references as to how he is living a nightmare trapped inside his mind as his body is being controlled for evil. This nightmare would "spill" into other people's minds, which would be a nice reference to why Darkrai induces nightmares in the first place. Other than that, though, I'm drawing a blank. If you have any suggestions, PM me so that you don't have to wrap spoiler tags around everything.
Third villain (I told you this was long). He understands that the "hidden evil" is trying to obtain the soul dew by using Latios and Latias, and therefore is trying to kill them. He's the misguided hero, in a sense, as his motive is to save what and who he loves. However, what he doesn't know is that Darkrai would eventually get the soul dew on his own (the latis can sense it, which makes finding it a lot faster), and therefore if he kills Latios and Latias there will be no one to stop Giratina and Darkrai when they come to power.
...Now that I look at what I wrote, I'm finding that I actually do have a pretty good sense of what I want from my characters, lol. It helped to actually write it out, I guess. Anyways, if you have any suggestions, like to point out a gigantic cliche or to say that something won't work or to suggest a different direction, please PM me as I said before. Thanks for reading all of that, as I know it was long.