We don't plan to support custom install locations because we believe where an app is installed is an implementation detail that users shouldn't worry about.
There seems to be a popular myth about separating applications and the OS on different partitions. Due to registry entries and other dependencies the desired separation of apps and OS is largely an illusion.
The way to deal with this inevitable entanglement of OS and application configuration is not some ineffective partitioning scheme. The solution is to make rebuilding the configuration cheap and painless via tools like Ninite.
The best argument we hear for this involves using small solid-state disks for the OS partition. However those will be getting larger quickly as the technology matures. Also, users will likely want their frequently used apps on the fast SSD too. Better to push large data files to rotational media.
This support article from Microsoft has some good examples of problems that can show up when default install locations are changed. We strongly recommend just using the defaults since those are the most tested and most standard configurations.