1. I can't figure out why the generators are generating bad code!

This is generally a function of unexpected modelling. For instance, problems with entity relations can have a root in a number of areas. Be especially wary of any code that you import with a reverse engineering tool. While substantially correct and it looks great, you can get a false sense of security and waste hours trying to understand why the code that is generated has no relation to what you thought you were modelling. If you are capable of reading it, the best source of the metadata is the XMI itself, not the rendering of the XMI within the tool (as that is often not completely accurate.)