Well my main reasoning behind it is the Hondata system, which you will need for proper tuning of your new motor.

Hondata will work with a PR3 and PW0, I believe the PR3 is newer, so get that. Less likleyhood of the ECU dying on you, etc...

Other then that the two are identical(?)
Both from B16a - personally I'd get Hondata right away and have it tuned as soon as she's broken in.