Yes, I can see that the notification feature is useful for people who keep gPodder running in the background all the time, but not for people (like me) who don't.

I use settings:

• Check for new episodes: Manually
• When new episodes are found: Show episode list

With the old version, I would run gPodder, click the "Check for new episodes" button, then end up at the list of podcasts to download (in my case, usually just one episode to download).

When the new version, I run gPodder, click the "Check for new episodes" button, just as before. However now I either have to be keep an eye on the screen and quickly click the yellow notification in the top-left at the correct time to reach the window showing me the new episodes, or if I miss that, I have to click the task switcher button then click on the yellow thumbnail window. For me, this is a decrease in usability.