[My initial list:]
speed for superhi-perf games
app store placement
[list compiled from other people's twitter answers; thanks all!]
pushing native notifications when they're not in the "app" (several people said this)
Hardware access (camera, GPS, NFC etc) - presumably solved for camera (webRTC) and GPS (Geolocation) ?
monetization. it’s hard to take £1 from someone online (many said this - both getting paid when someone "downloads" or "installs" an app, and also in-app payments
UI fluidity — e.g., scroll physics only fairly recently supported properly (wasn't this the Facebook reason, too?)
inability to present as installed app on non-iOS mobile platforms; cross browser dev is hard; no App Store discovery; avoid feuds
‘magic folders’ so you can’t store anything on the device (like Dropbox app)
if you want it to work offline [appcache inadequacies], also timely and concurrent audio.
place on someone’s home screen (possible with web but less intuitive)
Access to all the native device and services APIs of the platform is probably a big one. Probably ability to use native widgets too