Still, it has its fair share of weird choices. For shoot'em ups, for instance, I don't understand why you'd have Parodius or Twinkle Star Sprites in there, while missing truly genre-defining games like Dodonpachi.
I would've picked Cotton as the token cute em up instead of Parodius, but Twinkle Star Sprites makes perfect sense. It's a very unique mix of shooter and puzzle game, and a great co-op title. There aren't any other games like it. This list obviously aims for diversity, and it definately stands out (same as Ikaruga). That's a likely explanation for why Alpha Centauri was picked but Master of Orion 2 wasn't (or why there's only one Fallout/Thief/System Shock game, no Dark Souls or Tactics Ogre etc): two space strategy games on the same list would've been too much, so the other had to be relegated as an honorable mention (atleast I assume it is one). That's why JA2 and XCOM were picked but Silent Storm is an honorable mention. Though given that, the JRPG list seems too bloated by games that aren't different enough from each other.
Mushihimesama futari is currently the all time highest rated game on competitive shoot em up forums, and it's infamous for having the hardest final boss, so it makes sense that it was chosen to represent bullet hells and Cave's output, since Batsugun is there to represent foundational bullet hells and manic shooters. Still, the ratio between classic shooters and bullet hells is kind of skewed, you'd think that they could've fitted in Ketsui, one of the later Dodonpachi titles or Gunbird 2 or some other Psikyo/Cave title instead of R-type or Gradius.