You can use the new distroprefs feature of CPAN.pm.

Here's my file for Template-Toolkit:

--- 
match:
  distribution: "/Template-Toolkit-2\.18\."
disabled: 1
--- 
match:
  distribution: "/Template-Toolkit-\d"
pl: 
  expect:
    - "Do you want to build the XS Stash module"
    - "y\n"
    - "\QDo you want to use the XS Stash by default? [y]\E"
    - "y\n"
    - "Do you want to install these components"
    - "n\n"
[download]

You can also specify environment variables and command line arguments for every of the build phases (configure, make, test). And many many more things.