As much as I am starting like your new logos, it would be very cool if you could make the icons for native applications a bit easier to distinguish from each other. I do not have a tonne of things in my dock as of right now, and three apps with the same shape and colour is not that bad. But never the less I always select the wrong application when Alt-Tabbing etcetera.
Rant over, here is a screenshot:
I think just having the shape of the logo in blue would look great, and be a lot easier to distinguish. Especially as your native app suite grows with more additions.