When web-app DEVELOPERS finally get the whole offline thingie working, a web-first option will become much more of a real option...
/edit: Then again, I'm not positive if Google Chrome's "intalled web apps" often being shortcuts are developer's fault or Google's? I'd love someone with insight to tell us.
It's an awkward combination. By installing a Chrome App, the app can use more and newer (read: more privileged and untested) APIs. These can help make offline apps better. Sometimes they simply look like links but DO enable other functionality. This is the case with several of the Google Apps.
I agree that it's confusing and it's one area where Google could (and I'm not saying they will, I really hope they don't) exert themselves and use the Chrome Web Store as a way of gating "web apps" in Chrome (versus branded "Chrome Apps")
When web-app DEVELOPERS finally get the whole offline thingie working, a web-first option will become much more of a real option...
/edit: Then again, I'm not positive if Google Chrome's "intalled web apps" often being shortcuts are developer's fault or Google's? I'd love someone with insight to tell us.