Here's my problem with this idea:
I, like many people, listen to a lot of different podcasts. Dozens, in my case. I have a podcatcher app that puts them all in one place. That makes it easy and convenient for me. Some of the shows I only listen to maybe once per month when there's a guest on that I enjoy, or if I run out of new episodes of everything else. If each show required its own app for me to listen, I'd only listen to the ones I really, really enjoy and support, and the rest I'll do without or bootleg. So, in a sense, the individual app per show idea would be limiting the potential audience.
I'm already seeing this happen with Libsyn custom mobile apps[0]. There are a number of shows I listen to that have paywalls for old episodes which can only be accessed through subscription plans available in individual apps. $1.99 or $2.99 may not seem like much by itself, but if it's 10 or 20 shows you're listening to this becomes an unjustifiable bill.
The only viable alternative I see is the further growth of podcast networks, where multiple shows are available for one price. But, currently, this model is still too small and fragmented. Until the Netflix or Hulu of podcasts comes out, I'll be left to pick and choose which deserve my support enough to justify buying into their distinct "ecosystem".
Edit: I see that my points here were addressed in the paragraphs following the one I quoted, but I'm still not buying the idea that siloing is the best way to monetize podcasts.