I have sold a lot of both over the past 8 months. The biggest concerns I hear are the slow response of the wireless foot pedal on the Ulterra, hard to use around docks, structure etc. I have heard one problem of the Ulterra not stowing, at night, and that was a nightmare. Ultrex has had some foot pedal problems as well but all mechanical. They both have a few minor problems like the wire plug pulling out of the head, which does not affect performance; it is more difficult to add a DI or SI transducer to the foot with the Ulterra, but it can be done with purchase of few brackets. If you don't run the transducer cable correctly on an Ultrex it is easily cut in two on deployment. Spot Lock and i-Pilot functions are great on both models. I have the Ulterra on my boat which is great for putting a boat in by yourself, if you use the proper procedure and make sure it is working before you float your boat off the trailer.
As Pakjohn said, either one is great and they both have their pros and cons.
Be glad to answer any questions you might have on either model.