I can't speak for all those at are looking at building rather than buying a system but here are the two main reasons that we are currently building a system after using a purchased product for 3 or 4 years.
The cost per server for a purchased solution is a tough sell to managment, especially recently, however a backburner project is very low cost and can be used for all our current production, test and development servers plus any new server that are brought online without having to plea for funds for additional licenses. Not to mention with a home grown solution you don't have yearly "maintenance" fees.
Some of the tools are a bit of a chore to configure and updating to a new version will start the configuration process all over again. With a home grown solution we can focus on the metrics that we are most concerned with and store the data in a repository that fits our corporate standards so we can more easily generate performance reports for the business units to show what we are doing to enhance their server performance or to justify repacing or updating hardware.
Since all these comercial systems use SMO and WMI and the like to build there systems it isn't too much of a chore to tap into the same components to get the data we need. I have liked the system I have been using for several years but it isn't always everything I had hoped for and the licensing and fees are getting to be a tougher sell to managment every year.