Some ideas for a next major increment:

• Adopt the on() standard as set by Prototype and jQuery (et. al.), see #55. This probably should be done inside bean.js rather than ender.js and could potentially be encouraged as the standard interface to Bean rather than add().
• Reworked internal fixEvent() to improve speed by caching and applying 'fixers' for event types. See the newevent branch. There's some other potential changes that could be made to the copy-properties whitelist approach.
• Clean up the delegated events code, it's become a mess as a result of fixing bugs in this area (clone() not working, custom events not working, currentTarget set correctly). Search for __ in the code and you'll see the mess. Most, perhaps all of these special properties for delegated events could perhaps be moved into the registry. This would probably make #24 really easy. I believe that one() won't clone properly either so it should receive similar attention.
• Related to the above, nativeHandler(), customHandler() and del() could/should share more code, perhaps be merged in some way. Some of the delegate problems are as a result of properties not being available in the right place, del() is called inside add() but the other handler-wrapping takes place in addListener().
• Consider the relationship between add() and addListener() and remove() and removeListener(). The new registry took away a lot of the obvious reasons to separate them and the boundaries between their purposes is now a bit blurred.
• Consider possible replacements to the customEvents system that could be exportable. Perhaps a list of objects that contain functions that are called from various parts of the code that can modify objects or behaviour. customEvents isn't really flexible enough to export as a useful API and there's a lot of potential in opening it up to the ability to create custom events. See #36, #41, #50. (Perhaps this could be a 0.6.0 job because it wouldn't be trivial!)
• Don't increase minified/gzipped size, decrease if possible!
• Clean up the __beanDel code, it smells.