Google Apps has come a long way, but the apps still have a few kinks to be worked out. Kevin Purdy lists some of the drawbacks to Google Apps.
One day, when everything is right with the world, having Google Apps installed on your personal or business domain will be exactly like using Google with a Gmail address, just with a more legitimate identifier and better control.
But today is not quite that day. The viability of Google Apps has come a long way, and the apps offer a wide range of services. But using Google's and other vendors' web-based apps with a Google Apps address still requires overcoming a few kinks, or sometimes gritting one's teeth and waiting on a better day.
Here are the current drawbacks to Google Apps in the Enterprise, as I see them:
No Profiles, so no Google+ Support
Google + is likely a feature that's on its way, particularly the Google Profiles portion, as Google is all-in on Google+, and Google+ is headed to the workplace. However, moving and porting profiles from a personal Google account to Google Apps in the Enterprise is not always easy, as you'll see below.
Google Voice can't port from Gmail to Google Apps
In its original incarnation as GrandCentral, Google Voice was built on the very idea of managing multiple phones (work, home, cell) with one number. So it's somewhat strange that you can't transfer Google Voice to a Google Apps account, at least in the traditional sense. You can create a Google Voice instance inside an Apps account with a whole new number, and perhaps forward your old Voice number to the new one for a transition period, but a true transition is something that might expand Voice's use in the enterprise.
Limits on email addresses
Unless you're a government, school, or non-profit, Google Apps costs $5 per month, or $50 per year, for each "seat" you add. There's still a free option, but as of May 2011, it's limited to 10 users, admin included. Google has a right to, you know, make money from the hosted services they provide, but it leaves not-quite-tiny-, not-quite-big-groups with a strong temptation to simply create free Gmail addresses with linear usernames and work from there. It's a weird kind of curse: Gmail is so respected that handing it out as one's "official" address isn't quite frowned upon, even if there are real security and control benefits to Google Apps email.
No Google Checkout, so no Android Market purchases
Perhaps the best evidence of Google Apps' status as a nifty-but-not-quite-robust service is its lack of scaling with regards to Android. You can set up and sync an Android phone with a Google Apps account, and use all the same apps one would have access to in a browser. But Google's Checkout service only works with "personal" Gmail/Google accounts, not Google Apps. Buying apps through the Android Market, therefore, is a no-go. It would be mighty handy, for example, if everyone signed into an Android phone with a WXYZWidgets.com address could have pre-purchase access to certain key Android apps. Until then, the folks stuck in GApps/Android limbo will have to wait their turn.
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The general wait on new features
Even if you're working in a Google Apps instance where the "Rapid Release Track" has been enabled, Google Apps still means watching Gmail users and tech pundits get excited about the latest new Google-Thing, while you know you're at least a few weeks out from trying it. Google+ is just the latest example, but Google Apps users are likely used to the "coming soon" phrasing.
Before Google+, it was Google Buzz (which still remains a personal-only tool, if not all that necessary), and before the great Google Apps transition, it was just about every cool new feature for Gmail, Google Docs, and Google Calendar, among others.
Google has its reasons for keeping Google Apps users away from the bleeding edge of its release cycles - security, deployment costs, and stabilization among them, for sure. But as some folks see it, it often feels like Google's biggest fans and advocates are being left with an experience that's slightly less agile and exciting.