There's a page[1] describing why they created AlterEgo.
They basically claim everything else was too difficult for people to use - which is funny considering the other companies[2] using Google Authenticator. They also call it "1.5-factor authentication", which is kind of unsettling.
AlterEgo is a closed-source online-only service provided by MailChimp, while Google Authenticator is an offline, open-source, standards-based, two-factor security solution that anyone can implement on a wide range of platforms. You'd have to want less compatibility, less reliability and less security to use AlterEgo.
It's funny they say that, because google authenticator's git repo has commits going back to 2010, and AlterEgo was launched in 2011. Could be a coincidence though.
Edit: Nope. Just confirmed Google Authenticator was released in February 2011 [1], and AlterEgo was released May 2011 [2].
GA is just the better known implementation of OATH/TOTP. There are independent third-party implementations; I use a J2ME one, which works fine even with Google's own webapps.
If you follow that rationale your going to enter a spiral of reinventing wheels ad infinitum.
Just make sure that whatever you rely on can be substituted for another system and you're good to go. You depend on that service but on the off chance that it's discontinued your business is not at risk.
