Here is why, as of now, the ex is my top suspect. Some of it is based on facts, a lot of it is based on hearsay, but all of it is mere speculation until we get more information. That being said...
I get the impression that the ex cared a lot about appearances. It's one thing to want to remain cordial to your ex-wife for the sake of your children, quite another to not even tell your family about the divorce. Judging by what we've heard, it sounds like the husband was very interested in keeping the family together, even contacting a psychic for guidance a couple of months before the divorce was final. His social media is littered of pictures showing a family that is very happy and full of love. According to a mutual friend, they agreed to continue to appear married on social media for business reasons, though why it would matter to either of their businesses is beyond me. She's a realtor, he works at a company that makes plastic packaging. I don't think people care if their realtor is married, but who knows. Perhaps it could have something to do with the townhouse that they (allegedly) bought together and were hoping to sell. But I'm wondering if that townhouse was actually the one that Crystal planned to move into and the ex was just telling people they planned to sell it in order to keep up appearances. That could be where the "two townhouses" rumor came from.
Anyway, I don't think the uncle was lying when he said that Crystal told him her ex threatened her by saying she'll never leave him or their home. Crystal obviously got sick of playing house at some point, or else there wouldn't be a divorce. She opened up about her ex to her uncle as well as the friend that texted her before her disappearance. If the ex was still hoping to change her mind despite the divorce, he may have laid off of her a little bit--given her some space and the illusion of freedom in a last ditch effort to convince her that he's not such a bad guy. But if so this seemed to backfire on him, because suddenly Crystal was more ready than ever to move on. She got a new boyfriend that the ex didn't know about, but perhaps he could sense that she was truly slipping away this time. They got into an argument that resulted in her deleting a bunch of photos off of FB and blocking him, deliberately threatening his illusion of the perfect family. If he caught wind of her post about being the happiest she's ever been in her life, that certainly would have affected him and perhaps even sent him into a rage. And this would have been before he learned about the boyfriend or the cruise. So just imagine.
At some point they became cordial again (probably for the sake of the kids) but her certainly didn't stop trying to manipulate her. For example, the text he sent her on the eve of her disappearance that the daughter was hoping to see her before bed. That's quite the loaded text and would make any mother feel extremely guilty. Notice Crystal's reply to it though, saying she'll be there early in the morning. It's as if she knew what he was trying to do and wasn't falling for it. Imagine being him, realizing that you can't get her to do what you want anymore.
So all of that is what I would consider motive. IMO, he's the only person who has one so far. Things were going great for the boyfriend, and while a third party crime is possible, it's extremely rare.
How could he have done it?
The kids are still asleep. Crystal texts him and says she's on her way and asks if he has water. He tells her he doesn't have any water. An hour later he texts her again and asks "How much longer til you are here?" She'd told him she was on her way, so she should have been there already. I think this was the critical period where he did something to her. Perhaps he called her on the phone and offered to meet her halfway with the kids, close to the motel, but left the kids in their beds and met her on his own. Perhaps he was brazen enough to do it when she came to the door. But the lack of panic about her showing up is very telling. While everyone was freaking out about the storm, he could have covered up his crime. I hate to say it, but if there was a shallow creek somewhere out of the way from homes/businesses, placing her there would have ensured the storm covered up the crime for him.
I think that if it was a random person, we'd know it by now. She would have had to stop somewhere, and that place most likely would have had a camera. Boyfriend's work? Camera. Random gas station? Camera. Grocery store? Camera. ATM? Camera. It was immediately made public when they took that couple in for questioning, which leads me to believe that if they saw her with random strangers on a camera somewhere they would have made that public. Especially since we still don't know if she's alive or dead! But if it was her ex shown on a camera, it would make sense for them to not show their whole hand and instead use that information to get him to confess.
I just hope we get more information soon.
I'm sure people will be able to find some holes in this theory (which, again, is mostly just speculation). The two things that make me question it myself is the whole kid issue and him telling her he doesn't have any water. Like, if in my theory he's sitting there fuming mad that she didn't come home, wouldn't he want her there asap? Why would he tell her he didn't have water? So, that could be considered pretty contradictory.