I use Beyond Pod (with Presto!) mostly to listen to public radio podcast. This includes podcasts of specific programs with new "episodes" daily and weekly, and custom podcasts from NPR's Playlist. NPR's flash player in web browser lets users create their own playlist of specific stories or segments from All Things Considered, Morning Edition and other programs and then create a custom podcast feed (instead of listening to them in the web player). Because I end up with a large number (20-30) episodes in a given feed, Smart Play does not work well for me. Instead, I use Automatic Playlist to create a playlist from the feed (by playing the first episode).
Public radio podcast feeds seem very susceptible to the same episode being downloaded more than once (with the prior download going to archived episodes) and to old episodes showing up in the feed days, weeks or months later. This can be annoying. I have used different podcast clients on my desktop (Replay AV, Winamp or iTunes) and they don't seem to have this problem; it appears unique to BeyondPod. I can appreciate that sometime the podcast publisher "tweaks" the episode and BeyondPod treats it as a new episode (the desktop podcast clients seem able to tell it's not new) but I can update a feed a second time, immediately after doing "mark all as read" to get rid of a bunch of old episodes and I get some more old episodes showing up (not necessarily the same ones as a minute before).
I've gotten used to version 3.* and able to get it do what I want. Please don't change things again so I have to relearn the app again. Even if a new way seems better, there is something to be said for what's familiar.