"Flavor of the Month"
basically was the poster child for Gen 4 with being the only non-Legendary to get a theme based on them at that point and later continued to keep popularity through Gen 5 and alongside
and
were the big poster children for Mega Evolution as a major Pokemon. Zoroark would have been a flavor of the month choice, even Sceptile could be argued due to him being the big candidate from OR/AS and the missing Grass Starter for the trinity.
WAS a Flavor of the Month choice based on Japanese popularity (namely due to the anime) who would be easy to make from reusing
assets.
And if you forgot the Post-E3 interview, Sakurai stated that
was chosen by concept art far before Gen 6 came out because he really liked the design and wanted to make another Ninja character. His popularity from the fans was a coincidence.