I've been a user of multiple billing systems to date, and they have all had good things, and bad things. Blesta is my favorite system so far, however, as with every other system that I've used, I've noticed some areas for improvement.
I would make these avaliable as a plugin myself, however, I do not have the knowledge at the moment to make this happen..
Improve the support system: support Rich Text (or html) in tickets, and implement a WYSIWYG Editor for commenting on tickets on both the client end and the admin side.
Add the features of Support Manager Pro into the core of belsta; This would certainly attract more customers and seal the deal for them to use blesta.
I unfortunately had a couple more things, but cannot think of them at the moment, the first bullet is the biggest thing that i'd like to see added.
I'll try and update this if anyone mentions anything else, or if I think of any of those other features.