You do realize that it would make no difference if the game were on the web or locally on the phone, right? Why would putting the game on the web change the way the user interacts with the game? Your issue is an iPod vs iPhone interaction issue, and quite unrelated to web-based applications.
The problem with web-based apps is quite evident in this very example. Say, for whatever reason, I wanted to go to popcap's website. Uh, I'm automatically thrown into a game of Bejeweled with no choice whatsoever. It's unexpected, and it's not what I wanted. That's stupid. Web-based apps are encouraging websites to toss the iPhone into a specialty sandbox that may or may not be better than its original website.
Kinda like WAP, except that this loads slower.