Hi Nick,
Some answers regarding your issues:
--- Iteration planning ---
You are able to use the phase attribute, but the tool does not really have any managing abilities for phases. This means that a Software Development Plan needs to be written to describe and plan phases.
--- Model organisation ---
The default views can be deleted without worry, as far as I can see, the default views concern only the icons used for the views and not any functionality.
--- The way to go ---
The way to go is depending on the outcome (deliverables) you want to deliver. Because of the tree organisation of a project, you have to make some choices. The way I did organise the project is purely based on the documents that need to be delivered (J-Std-016 / Mil-Std-498 in my case). This corresponds to phases like system requirements, system design, software requirements, software design, etc. This will be the same for UP, I guess. This results also in a tree underneath views & packages being the responsibility of one project, development group or analyst / developer.
If the target of the model is solely for code generation, the model will probably look more like the actual code organisation (modules, components, etc.).
--- Summary ---
My personal feeling is that EA can be customised extensivly and it will therefore fit many processes and deliverables. If you have more questions, please reply.
Greetings,
Tjerk