I might have said what is missing, what is lacking, but I rather keep it personal and also as a sorted and dynamic draft (*)
Here is my short list on what I dislike about GApps?
- Shared Contacts across the Domain: Incomplete, inconsistent, cumbersome solution for sharing contacts. No actual contacts address books for sharing with different access levels across domain users and groups.
- Document to Pdf issue: when downloading a document as a Pdf (or emailing as a Pdf attachment) the format got wrong - luckily when printing / saving to Google Drive it's fine.
- Current default Gmail Inbox view by categories: Great idea with two major flaws, not showing unread messages on each category (just the most recent) and no easy way of showing unread first within each category.
- The new hangout widget in Gmail instead of previous standard chat that allows you to call a computer, among other features. (still using the old chat, do you?)
- No columns option in Google Docs Documents: Simple, there is no columns format when creating a document in Google Docs.
- No comments on posts in Google Sites: Only users with edit access can comment in a Google Site page. It would be much better if any authenticated user with view access can comment.
(*) I will keep this list updated as I change my mind or Google Apps does better, and also include my clients and collegues feedback.