This system is very intuitive for the user which increases the chances that your clients will actually use it! If they use it then you will get the benefits of both being able to stay organized and staying on top of your billing/cash flow which is crucial to your operations.
Obviously much time has been invested in this system and I think it is a great value for a one-time payment type system. A few more valuable suggestions to the developer from a system ownership standpoint and it will truly be a premier extension that any project manager cannot do without.
A few things that I think could be useful:
As you are immersing your self into a new system you will want to be sure that all of your e-mail templates look just right and convey the right message. It would be nice to have a development mode where it prompts you before sending out one of the automated e-mails and/or allows you to preview the e-mails that are about to be sent. It is a bit nerve wracking to wonder whether an e-mail is being dispersed. After a certain amount of time you could turn off that development mode.
Option to CC owner on all e-mails. This will allow you to audit the outgoing mail on a regular basis.
Add a PayPal link to new invoice and invoice update e-mails when PayPal is the method. This prevents your customer from having to log in to pay the invoice. I performed this change on my own system.
TinyMCE is hard-coded in which means you cannot use JCE or other. Would be nice to have that option.
The extension seems to have the potential to be outstanding. Just figured I would give my two cents as it seems to be getting a bad wrap from some folks.