I just started using Agenda. It does look like the integration with Calendar shows every calendar I run in the Calendar app. I run many calendars in my Calendar app and hide a few of them because I only need to check them occasionally. But Agenda doesn’t care, and doesn’t seem to give me the opportunity to hide events from calendars I check only occasionally. This make the calendar events view in Agenda very confusing for me, with many items being displayed that I could not care less. I think a better integration with the Calendar app would give the user the opportunity to hide a few calendars from that app.
Said that, I should say Agenda looks very pretty. I see some people complain about the font and its size. I love it, but of course the ideal solution would be to give Agenda access to the system fonts and let the user pick the font they want.