The first Halo was quite a unique shooter in any respect for anything of the time. Halo 2 was also quite the online innovator on consoles. Call of Duty's online setup wouldn't be much without that. But still there were games on the PC such as Counter Strike that were doing that already.
Metal Gear really provided a unique experience along with a different way of telling a story that really has never been exceeded or surpassed. But once again like Halo, after such said innovations it didn't really expand further. Which is fine, as it made evolutions within its own genre but not really a continuous influence on the industry.
But looking at it, I'd say that Halo has been the most influential. Now that doesn't mean all that has been positive of course but it has had the most influence. First, without Halo there would be no successful Xbox brand. Without the Xbox brand there are quite a few things we'd be without that has come from it. Secondly, it essentially started the idea of a "modern" shooter on consoles and PC. Not to mention really created a sub genre of mixing an adventure game along with a linear "level to level" shooter. Wasn't as full as Metroid Prime but still. Then of course the online setup of Halo 2 paved the future for online console games forever while something similar for Halo 1 on PC.
Halo has had a huge impact on this industry. So has MGS but and most of MGS has definitiely been in an inspirational development standpoint kind of like a lot of Miyamoto or Shinji Mikami's games. And I guess that's what separates them as legendary developers compared to the rest. But on an entire industry standpoint, I have to go with Halo. If it was pure development, though, no questions asked it would be MGS.
