I agree..Not to be mean or anything but... Jiraya hasn't been in town since then. Plus, Jiraya tutored Minato it's logical that he knows about him.
Jiraya hasn't seen Shikamaru in action so that's logical he would state such things only about Minato.
See the difference... While Jiraya said Minato is a genius, Minato said about Kakashi that he is a ninja prodigy being able to create chidori at such a young age. And the third lived to see all 3 of them and stated that his intelligence (Shikamaru's) is the highest in Konoha at that moment. But when it comes to tactical plans.
Each of them are in their own league.
I won't give you the fact that Minato wasn't bam, but while he thought at a single possibility, Shika did like multiple ones in a battle and was able to calculate which one suited the situation. And that in a short time as well.