I have a question related to PKI Infrastructure: should an organization go with Microsoft PKI or an independent separate PKI Infrastructure? Is there any licensing restrictions if I use Microsoft PKI Infrastructure? Or should I get an independent PKI infrastructure from a vendor that offers PKI TSA and SP (Signature Proof) Infrastructure?
Very hard choice and it depends on your requirements.
I am a fan of the Microsoft PKI stack, it is very easy to use and manage. That aside, if I am doing anything related to Active Directory / per user certificates etc, the Microsoft PKI is the best on the market, as you expect, it integrates well and seamless. I love it!
There are alternatives out there, but unless you are willing to pay for support or know it very well, I would stay clear - at the end of the day, the Microsoft CA stuff does everything I could need.
As for licensing, I always assumed it was free with a valid Windows (server) licence in the same way as DHCP or DNS server can be used to service/manage as many clients as you need.