A couple of issues I do see still with HTML5:
- From a serious developer's perspective, let's face it: JavaScript is truly truly dreadful. By rights, it really should have been allowed to die its death in peace. Many developers, including myself, reluctantly put up with it for some tasks because it has gathered such industry momentum as a cross-platform solution. It 'runs in the right places' but from a developer's perspective, it's really not very apt for remotely complex applications and, were there a choice, not really what you'd like to be using in most cases.
- HTML5 doesn't solve the problem that native apps still have a privileged position on many devices in terms of App Store discovery and access to some native functionality. The latter may not be huge issue for many apps such as simple games, but the former may be. (It's probably true that raw performance isn't the issue it used to be, on the other hand.)