Alpha 3 includes various updates to unify language and fields across the user interfaces, with a much improved order edit form that is actually useful now (using vertical tabs, no less). The customer profile reference widget was improved to actually be usable on order edit forms, but it still needs a little bit of love to avoid creating duplicate profiles when it's not necessary.
We also fixed currency handling in relation to the different types of Price field widgets and managed to get every currency defined with much better currency formatting thanks to das-peter. He also helped get our Entity API and Rules integration a little more up to date with more issues pending review in the queue. : )
Work begun last release cycle on the Payment system was pushed forward, with a lot of work done to support credit card payments on-site. A proof-of-concept module was released in the form of Commerce Authorize.Net that you can use as a guide to developing integration with other payment gateways.