How to choose between Bean, Boxes and Fieldable Panels Panes?
It's perfectly possible to make a D7 site without blocks if you can live without dashboard. 
Our new - content driven - site is being built on panels with workbench as a suitable (for us) alternative to dashboard. Arjan appears to already understand this. 

On to the alternatives.
Read Your site should be full of beans.
The problem with boxes is the danger regarding overwriting existing content when using features. But read Fabian Franz's comment in the same article. Beans has many options. I'm not comfortable regarding management, scalability and performance. Hardcore developers that are fluent with panels use Fieldable Panels Panes. Fieldable Panels Panes lack documentation and examples.
What should get everyones focus and effort for D8 is the wscci-initiative. It allows for REST-calls, including for example DELETE. This could permanently tackle the problem of overwriting site builder configuration on code rollouts.