Eclipse integration, highly customizable, can be used for requirements gathering, issue tracking, ITIL solution, reporting solutions are great, built in dashboards or ability to create customizable dashboards for the organization.
Distributed version control systems are a lot more convenient when developing features in parallel and releasing hotfixes. Also Atlassian's Git and source tree provide protection from checking in on the main trunk and allows people to comment on specific lines of code.
I do not make decisions on what tool my company uses. I am just the user of the tool and such decisions are not handled by me. If I were to make such decisions, I would definitely renew MKS, considering the amount of data we have stored in MKS and the current number of users who are familiar with the system.
PTC Windchill RV&S (formerly Integrity Lifecycle Manager of the Integrity suite) is an MBSE (model-based systems engineering) suite. The former Integrity suite contains an Asset Library which supports systems-of-systems approach to design (i.e. linking models into higher-level models that subsume them), a Process Director which is designed to articulate, manage and improve the design process, and a Modeler for visualizing and controlling the product design process. The Integrity suite is rebranding and being integrated into PTC's Windchill product suite.