Maybe someone is interested in:
I got a similar problem with Mail.app in Mac OS X 10.10 Yosemite and a surprising solution.
It took about up to 2 minutes to start Mail.app and display my messages in my 11 accounts. Too long, so i started with deleting/reorganizing the envelope index but with only less effect. It still took about 1 minute to get the Mail-Window, although the messages were now displayed instantly.
Disappointed I quit Mail again and I saw the accounts window closing after the Mail.app main window and I thought: "Maybe that's the solution!"
So I reopened Mail.app (2 minutes ;-) and opened the tucked away accounts window (It was always behind the main window of Mail.app for some 5 days, since I changed a setting!) and closed it properly.
Now Mail.app opens instantly again! 🙂
I hope this helps some other having the same strange problem.