I'm no Nagoshi fan in that I've played very little of his recent titles (have only played a bit of Yakuza 1, all of Yakuza 2, and don't equate Binary Domain with it), yet I loved Binary Domain. Was it this mystical "SEGA feel"? Nope! In fact I can explain why I liked it: I loved the gameplay, especially the boss fights and the enemy combat. I loved my team members (Faye, Cain and Bog Bo). I liked the story and character interactions. I loved Cain (mentioning him twice).
Maybe I wouldn't have been so quick to TRY the game had it not been a SEGA title, but if I played it without the knowledge of it being SEGA, or if it were from Capcom or Konami, I would have loved it just as much.
So, in my opinion, is it merely a "good" game that is pushed to A+ due to some "SEGA feel" and cult of Nagoshi? Nope! It's just an honest to god awesome game. The only downsides were: speech recognition & online multiplayer. However, for speech recognition, even if it worked perfectly I wouldn't have used it because I play the game late at night and don't like yelling at the TV. I use the controller and on-screen text. As for online multi-player, I think it's unnecessary given the awesome single player.
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I still don't get this "distinct visual style". Sonic looked like nothing I had seen before, and with each SEGA franchise I encountered from there on out I was continually impressed by new games with their own unique visual style. I didn't look at stuff like PSO, Samba de Amigo, JSR, Shenmue, SC5, Panzer Dragoon and see a familiar style from a past SEGA title, I saw something new and fresh and unlike any of the past SEGA games I've played.
The only way I'd say SEGA has a "distinct visual style" is that each franchise has its own distinct visual style, feeling like something very different from the games that came before. But I'm not sure if thats what you are arguing. And if it is, "distinct visual style" isn't the right term. It's more of a lack of distinct visual style and an openness to a number of styles.