In JBIDE-3426 we was trying to find good solution to give possibility to modify generated annotations.
The solution for JBIDE-3426 does not look good - cause here there are some complexities:
1) here you edit annotations - not relations;
2) as result there are 2 rows per relation (it represents the same 2 associations);
3) it looks complex for use;
to display form like JBIDE-3426 - we could provide an option;

Once more - interface for JBIDE-3426 - is interface with possibility to edit particular annotation;
to simplify we could edit relation:
1) we could define relation between entities
2) then we could spicify properties for this relation
the simplest gui for this - is a table like in JBIDE-3426 but with other columns name and order
Possible column names:
Relation | Owner entity | Reference entity | Owner field | Reference field

here is possible to find ideas to simplify interface - google for this:
==> [BEA Workshop Product Family > Hibernate Tutorial: Generate O/R Mappings]