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Mikrotik is a router device , it can be hardware like Mikrotik router Board or Software. Mikrotik operation in Internet connection category , it can control in bandwidth , Limiting user , manage wifi networks , and compiles between more than connection from different ISPs .
Windows server is Operating System used to build Microsoft Infrastructure like DHCP, DNS, AD, File Servers, and CA.
Mikrotik Device is a Route. With a Mikrotiki device you can route your local connection through internet, make VPN connection with security. You can easily manage your clients bandwidth and many more. Mikrotik is a very cheap router indeed about 15 times cheaper than Cisco.
Other hand Windows server is a Server OS. You can start any service related to IT industry from Active Directory Domain service, FTP, DHCP, Internet Information Service and many more. It is a NOS(Networking OS ) for start and configure a service you need. Windows Server is a Costly OS.
Mikrotik device is used for manage bandwidth, internet access and as a routing device to route and manage internet traffic, on other side, WIndow server is used to manage file server active Directory used and computer management.