apple id on two phones

You've answered your own question

All the pictures I take end up on her phone and vice versa... She does not have her own apple id.

Because your two phones are signed into iCloud as you they behave as if they are both yours.

To set up her phone independently of yours she needs to sign out of your account on her phone and set up a new Apple ID on her phone and sign into that account on her phone.

It should be a email address she has or she can get a new email address if necessary.

As long as you are both signed into the same Apple ID, if you delete a photo from her phone, it will delete from iCloud, and your phone. The same if true if you delete it from your phone.

If syncing photos with iCloud, ensure Optimization is turned off in Settings/Your Name/iCloud/Photos and/or in Photos/Preferences/iCloud. Then make sure full resolution photos are on the device/computer. You can then go to Settings/Your Name/iCloud and turn off photos syncing.

For your wife making the change in her ID.

Apple ID - create a new.      

Apple ID – Create         

Family Sharing.         

Family Sharing - Set up.        

When changing to the new ID, there may be some data loss, but you can minimize it. If syncing photos with iCloud, ensure Optimization is turned off in Settings/Your Name/iCloud/Photos and/or in Photos/Preferences/iCloud. Then make sure full resolution photos are on the device/computer. When signing out of iCloud, if asked whether you want to retain data, choose yes. Messages conversations will be lost if they are addressed to the ID. See the article below for other places that the old ID should be removed. See Winston Churchill's response in the below discussion. Also set up Family Sharing between the IDs to keep access to your apps/purchases. 

How to switch Apple IDs on your iPhone or iPad.      

How to transfer all files from one iCloud account to another.        

What to do after you change your Apple ID or password - Apple Support.     

If they were sent to her current telephone number, she may be able to keep those after she adds the phone number to her Apple ID, preferably before swapping the ID on the phone. I'm not sure exactly what will happen.

Make sure the photos are full sized and not thumbnails.

If there are previous Messages conversations on the phone, when you change the Apple ID, they will be removed.