Working in Professional Services for another major enterprise application, I could really see this being the fault of either party. I think many in Professional Services (myself included) take a pragmatic approach to implementation. The focus is on getting something going that meets 90 or 95% of the requirements with a healthy dose of skepticism that anything beyond that is worth the cost. At some point, the customer has to pull the trigger, adopt and adapt. In the course of doing so, they will discover shortcomings and advantages that weren't envisioned initially, and the effort and cost of pursuing perfection initially can be saved for follow-up effort once all that real-world feedback is collected.
I have found some University customers tend much more towards wanting the "ideal" solution on Day 1 and as a Professional Services provider, going that last 5 or 10% of the way to perfection can be an extremely frustrating, money-losing endeavor.
At the same time, none of the above can be encoded in a contract that would ever get signed, so all you can do as a Professional Services provider is choose your customers wisely and know when to require time & materials contracts.