1. The ability to change the URL from default didn't really work for me.  I thought it might be a DNS issue, but after 24 hours it still will not go to my page with the 'sites' subdomain.  This seems to be something that is fixable since it follows the same method as the other Google Apps areas.  But still disappointing.
2. They gave me temples, great.  I want to edit the CSS.  Still less control over look-and-feel than Wordpress, or a hosted solution.  But I can manually change colors used on the page.  Still, that seems like a hassle to redo every time I have a new site and I need a consistent look-and-feel.
3. You can't change the site's path name.  You can change the title that appears on the page, but that doesn't change the name in the URL.  That could be annoying.
4. The big deal for attacking SharePoint is the Create Page > List feature.  Here are all of the choices for custom list data types:  Checkbox, Date, Dropdown, Text.  The dropdown is text only, no lookups or calculations.  And no default values.  Not even description text for the fields!  There is no way this replaces MOSS.  I live by the ability to create custom lists with 16+ datatypes.
5. Widgets vs. webparts.  Google has a ginormous library of everyone's junk widgets.  I am rarely impressed by these and there's nothing close to the CQWP.
6. No Content Types.  No document templates.
7. No metadata for uploaded files, not even ones in the 'File Cabinet'.
8. No linking to uploaded documents in the dialog box, only pages or URLs.
9. No auto-build navigation or header templates.  Unless you manually create your own navigation on every page, the Site Map is the only way to find things.  When was the last time you were forced to use a Site Map to navigate?
10. No links to users.  Everything in MOSS that is done by a user has a link to the user's profile.  In Google Apps there's not even a member's page to publically show who uses the site.  I don't think you can even use it for a wiki at that point given all of the controversy about who updates what on public wikis.

Meh.

*EDIT*

I now see how the breadcrumbs work and how navigation is built in Google Apps.  It's not bad, I just didn't "get it" on first look.