Thanks for the suggestion.
We like the idea of adding padding option, so here is a new beta:
https://dl.dropboxusercontent.com/u/13064071/plantuml.jar
This beta works with the following diagram:
@startuml
skinparam ParticipantPadding 10
skinparam BoxPadding 20
box "B"
participant Alice
end box
Alice -> Bob : hello
@enduml
This kind of modification is quite easy to do (when you are used to PlantUML code...), so we did it directly.
The setting can be set in pixel only (which is consistent other values).
Other padding settings may be implemented on demand, so please ask!
Regards