So I'm having a little trouble with getting Wiser crate trained. I started with a big wire crate with the divider. He slept fine in it the first couple nights but after that he wanted nothing to do with it.

I have done everything I can think of to make it more comfortable for him. I use good treats, chew toys, bones, leave the tv on, a blanket over the top to make it feel more "den" like, and I even leave my shirt for him so he can have my scent. He hates it when I leave for work in the mornings and the absolute max that hes in the crate is 4 hours.

I have another (smaller, plastic crate) that he sleeps in thats in our room. At night he knows it time to go to bed and he walks on in and goes to sleep with minimal crying/whining.

I'm afraid that having the 2 crates has caused him to think of his wire one as the bad crate (even thought I would NEVER use it to punish) and the small one as the good crate.

Any suggestions or advice on how to get him to like his wire crate more??

Also, he will pee in his wire crate no matter how long that hes there alone, but he has never done anything in the night time one.

He probably knows that the wire crate means that you are leaving, so he has associated that with that crate, and that's probably why he isn't happy. With the other crate being in your room, and you being in there makes that crate more comfortable for him. Is there a specific reason why you need to have two? I would use only one in your bedroom and for everything or even more it around if you need to. That way he gets used to one crate, whether your around or not.

We got the small plastic one for the vehicle while hes a puppy and just tried him in it one night and he seems to like it so we continued to use it for sleeping. We have the wire one because the way hes growing, the small one isn't going to be useful for very long so I want him to get familiar to the other one for when he gets bigger. I kind of assumed that the wire crate would be better for him during the day because it's bigger and he can move around more freely.
I guess I am a little fearful that using the small crate during the day will make it less desirable to him in the nights.

I would suggest starting over with the crate training and only do the wire one. There is nothing wrong with the wire ones, but I think he just associates it with you leaving and that makes him upset. So if you start over, and only use the wire one then eventually he will learn to like that one for sleeping and for being in while you are gone.