I don't have a strong opinion one way on the matter since I don't have any experience with the launcher.  I think I understand the issue of the Windows installer providing "release-independent" components (and, FTR, the OS X installer has a somewhat similar issue although the launcher there is believed to not be used much at all).  Whether we should change the defaults for future releases of 2.7.x and/or 3.5.x is probably ultimately up to the 2.7 and 3.6 release managers though I expect they would go along with whatever you all recommend.  If it does make sense to modify py.exe for 2.7.x and 3.5.x, then perhaps the corresponding change for 3.6 could be deferred until after 2.7.11 and 3.5.2 are released, which should be before 3.6.0a3, and all have consistent documentation of the changed behavior?  It's not perfect but at least all of the most recent binary releases would be consistent.

A somewhat unrelated comment on the patch:  will it be clear to users what is meant by "latest version installed"?  That is, what is meant by "latest version" in each of these cases: (scenario 1) install 2.7. then 3.5, then 3.6'; (scenario 2) install 3.5, 3.6, then 2.7; (scenario 3) install 3.6, 3.5, then 2.7; (scenario 4) install 3.6, 2.7, then 3.5.