So I originally read your post to imply that you feel MGS only appeals to Stealth Shooter fans, and you said I was wrong. Then after I apologize, you reiterate that you think MGS only appeals to stealth shooter fans.
So that we are on the same page, let me ask you some quick yes/no questions.
That should clear up the confusion :)
1. I consider stealth and shooter to be two seperate genres. MGS4 is primarily stealth. It uses guns yes, but so does Rachet and Clank (hell even Mario has cannons). Essentially, MGS is a stealth game that appeals to stealth fans. It will of course attract some people that are fans of shooters, but then so did Hour of Victory, so anything with guns can capture a small piece of the shooter audience. I believe that the stealth genre at large is shrinking in terms of its influence, but MGS practically owns the genre now, which bodes well for the 4th installment.
2. Once again there are not many stealth games out there anymore (even though most shooters incorporate a stealth section these days (CoD4, GeoW)), so I do consider the market at large to be more and more niche as time progresses. As I said above though, MGS in-and-of-itself cannot be considered niche, as it owns the market with this genre.
3. I didn't bring Bioshock up, and I don't think it is that relevant really. It is certainly a more conventional shooter (at least compared to MGS4, as Bioshock isn't exactly conventional), but this also means it faces far more competition than MGS4 does. It is often said that Splinter Cell: Conviction (Which could now wait until 2010) is Microsoft's answer to MGS4. The truth is, Splinter Cell is the only competition to MGS4. Bioshock may appeal to a more broad audience than MGS4, but that audience has far more product to look at than the stealth audience.
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