In many ways, Kougami vs. Makishima is like another famous Gen-wrote anime feud: Kiritsugu Emiya vs. Kirei Kotomine from
Fate/Zero.
On another thread, I wrote that Gen has a very good grasp on what's entertaining and what's not (in a "general audience" sense). Gen prizes consistent characterization, and will not sacrifice that purely for entertainment gain... but to the extent that he can have characters act in-character
and in a very entertaining way, Gen will go for that.
I think that Gen realizes that people tend to love pitched one-on-one combat between two closely matched and ruthlessly fierce competitors. This is especially true if there's excellent buildup to the fight, and/or if the fight has an ideological/philosophical element to it. Kougami vs. Makishima, Kiritsugu vs. Kirei, even Sayaka vs. Kyouko (from
Madoka Magica) are all like this.
Having two characters debate things out can certainly be interesting, and I think Gen gets intellectual appeal as well, but it was always clear to me that Gen wanted Kougami vs. Makishima to be his "next" Kiritsugu vs. Kirei. His next extensively setup climatic fight scene that would be a treat for the eyes and a stimulant to the emotions. Gen is one of a precious few anime writers today that I think
gets what makes Hollywood action movies so appealing to many viewers, and has managed to incorporate that into anime narratives. If there was ever an anime equivalent to something like the
Die Hard films, it would almost certainly be wrote by Gen.
To be fair to Makishima, I'm sure that if Kougami had chosen to debate him on the actions he was taking (or to talk on just about anything), Makishima would have been more than happy to oblige. But in Makishima's mind, if you can't have a riveting conversation with another interesting alpha male, the next best thing is to have a riveting duel with him.
As cultured, intelligent, and well-read as Makishima is, he's still very much
a man. Defeating his latest (and best!) curiosity and target was no doubt thrilling to Makishima, just like an amateur wrestler would find it thrilling to defeat a strong and worthy adversary in order to win an Olympic Gold medal. After defeating Kougami, there's little doubt that Makishima felt "on top of the world". He was in an uniquely vulnerable state of mind to be taken unaware, and Akane seized the opportunity.
I wouldn't weigh it too much against Makishima, though I hope we get to see more of his intellectual side before the anime is over.