There is not an alternative to Google Apps Mail, which is free, configurable, and powerful.
Currently the only way of swapping primary domain of Google Apps is – remove the alias domain and re-setup as new.
In order to keep receiving emails during swapping primary domain, I have to find another email service provider for the transmission period. I am not surprised I can not find any. Google is good, which is why I am using it, but its uniqueness is not a cheerful thing for business. I have never practised on a mail server just because google apps mail is taking care of everything.
It challenged me finding another email service provider, and finally I gave up. I used email forward service from my domain registrars and forwarded incoming emails to another google apps account.
Google offer 50 users apps as standard for free. When my business grow over this figure, I prefer my own mail server(s) rather than paying google. It is a shame to be pushed to pay someone.