I was just shown my Clincheck 3D predicted results for Invisalign and my end results look worse than when I started (Photo)

In my opinion, your concerns are valid.  My suggestion is to schedule a time to talk to your provider in private and tell him that you are not happy with the end result shown by your Clincheck 3D prediction.  It possible to do what is called a "mid course correction" to change the expected result of your treatment.  That said, I would be a little concerned about continuing treatment with a provider who would accept that outcome given your initial problem.  Successful clear aligner treatment is completely dependent on the skill of the Dr to determine the best final position of the teeth.  In my opinion, the 3D prediction was not the best final position given your initial bite.