Being smart and being a genius are two different things in Narutoverse. :|
The original word is Tensai(天才) and it's a slightly different concept than the English word genius.
It's not about sole intelligence. It covers the concepts of being a prodigy, having a natural gift, being exceptionally good at something and so on. That was the context in which Jiraiya was referring to Minato.
Neji, Lee, Oro, Kakashi, Sasuke, Shikamaru, Itachi, Gai, Shisui, Minato, Naruto and probably a couple of more ninja that I forgot to list have been referred to as geniuses (tensai) by someone in the manga.
We can't pit them all up against Shikamaru when it comes to comparing their smarts.
It has been stated that Shikamaru possessed an IQ over 200 points.
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Although Minato obliterates Shikamaru when compared overall, intelligence-wise Shikamaru takes the cake.
100% agreement.
In addition, intellect comes in many forms.
For example, academic intelligence is not completely synonymous with creative intelligence.
Also, intelligence is diverse (and dynamic) even within a singular discipline.
For example, within the field of chemical engineering there are those who are particularly well suited for industry and those who are better suited for research.
Consequently, multiple characters in the Narutoverse can be geniuses, yet can't necessarily be directly compared due to intelligence being present on varying levels.
Knowledge is merely stored information.
Intelligence is best defined as the ability to acquire knowledge and retain that information.
The more rapidly someone can learn and the longer someone can remember that knowledge, the more intelligent they are.
Wisdom is one's capacity to apply appropriate discernment regarding the knowledge birthed from experience.
Well Shikamaru and Minato are geniuses in different ways. Shikamaru in improvising and tactics while Minato in learning and developing jutsus and seals and we know hes good at tactics and improvisation although not as much as Shikamaru in that sense.