Whether it's worthwhile getting an expert opinion on the "health" of another's patent application depends on what you hope to do with that information and what that's worth to you. I can estimate cost to evaluate someone else's patent application and I can estimate a degree of certainty of such an evaluation. Whether that's worthwhile depends on what you hope to do with the information.
If that one fails, it doesn't necessarily mean that you won't have other patents to contend with.
Contacting the inventor isn't always the best strategy. Some published applications don't accurately reflect that the application is assigned to a company. You may find yourself corresponding with a Microsoft engineer about the prospect of going into business as a competitor to his employer. How the engineer would react is uncertain.
Re your last question, yes, you're missing something. There are nearly (over?) 7,000,000 patents issued. They don't cover things like "VoIP". They cover things much more specific than that. Each might cover a very specific type of VoIP, a specific enhancement, a specific tweak or improvement, etc.
I don't know if Skype has a patent on their particular type of P2P VoIP, but maybe they do. From what I understand, they're approach is quite different from what others have done in VoIP. While other groups were debating the particulars of a VoIP dialing system (assuming number-based dialing approaches to work with conventional telephone equipment), Skype bypassed the whole debate by using alphanumeric IDs (ignoring the assumption of standard telephone equipment) and a P2P structure, bypassing the collection of ports typically required for a VoIP connection. So far, it seems to be a successful design. Will it ever branch out to where we all have Skype phones around the house? Maybe.
It all comes down to the claims. If the claims of a patent application recite something that's new and not obvious, you get a patent (assuming all the other requirements are met). In fact, before you get all worked up about that application, read the pending claims and see if they describe what you want to do. You can probably see the Office Actions in which prior art is cited against the claims. Look at those documents, some of which are likely patents. Look at those claims and see if they describe what you want to do.
That would be a good start.
Regards.