Based on the previous hell of helping a friend create a Skype account by using their Microsoft and Facebook accounts to login (ended up creating three separate Skype IDs, a full one, a live: one and a facebook: one, which was resolved rather quickly thanks to support), I consider this the best way to join Skype:
- Register an account as normal, not using the Microsoft or Facebook connect options,
- Complete profile, then download and sign-in to the Skype client with your newly created account,
- Sign-out of Skype client, then sign in and merge with Microsoft account,
- Repeat with Facebook account if you wish.
With regards to email notifications, the fact you can sign up for Skype without having a Microsoft (@msn, @hotmail, @live, @outlook) account probably means they weren't going to include email notifications in Skype anyway (though they may add it in the future). I doubt this will happen, considering Microsoft seems to be pushing people towards Windows 8, and the Mail app (and Outlook 2013, when it's running) is (as far as I'm aware) already able to push toast notifications as new mail comes in. The desktop Skype application does have
extension capability, so maybe someone might make an extension for Skype for this feature.
Most of my friends appear to have abandoned their Microsoft accounts in favour of Facebook anyway (for instant messaging).