Because Raikou is not as common of a phazer as Suicune/Skarm, both of which wail on Scizor all day. In addition, if Raikou happens to be active against Scizor, you can bet he sure as hell won't be scared away by Scizor. Raikou is the only phazer Jolteon can't effectively setup against.
HP Flying is mainly for taking out Heracross along with the OHKO potential on Egg. HP Bug only guarantees an OHKO on Egg.