I completely agree and this is very frustrating. I've been working with an integration that is a complete mess and it would be easier just to start over but I can't.
Agree. Here's the key point: To be an enterprise-class solution, Marketo has to enable change and growth. Even the best-planned integration will need updating as business requirements are refined. I get that mapping database fields at this "metal against metal" integration point is complicated. But as a first step, at least give us the UI to capture the desired remapping and then submit it to Marketo Support for review and implementation.
To help you feel better, create a program in marketo, add plenty of assets and then clone the program. The go back to Pardot and try to clone a whole scenario