Well the questions in the title.

As you all know I am a pessimist in terms of anything PS3.

so I never expected MGS4 to get over 3 million, considering low userbase, but how did it outsell MGS3? isn't it shocking?

Its not overtracked I hope

   Higher userbase doesnt necessary mean higher sales for software. MGS3 was the 3rd MGS game on PS2, there is such thing called saturation.

   Gran Turismo 3 > Gran Turismo 2, Final Fantasy X > Final Fantasy IX and so on. 1st title on a platform often does the best, even if the latter title is superior (like MGS3 is considered better than MGS2, yet sold much less)

MGS4 sold better than MGS3 specifically to tell people like you that "low userbase" can still warrant a 3rd party exclusive

but GTA 4 has sold less than GTA:SA (all versions combined)

@rei

that is very interesting

but FF9 & FF12 both released after people new FFX/FF13 were coming (I mean after the trailer for FF10*FF13)

PS3 has a smaller game library than the PS2, so more people are willing to try out a critically acclaimed sequel of a franchise they haven't played before. Also because of this, MGS4 has less competition than MGS3 did, so it's easier for it to rise to the top. And since MGS4 was on a newer system maybe people who only played 1 or 2 of the earlier games wanted to see how MGS would be done differently with more powerful hardware and graphics.

@The Xbox Man:

Well, it doesnt apply to all games. GTA sales were indeed only growing as PS2 userbase increased. That probably has to do with lots of casual players being interested in it. But then again .. same can be said about Gran Turismo.

I really dont have a proper explanation for this. But I am quiet certain that MGS is one of these franchises that do best with a 1st title on a platform.

MGS3 was overshadowed by GTA:SA when it realised. MGS4 had more hype behind it.

Metal Gear Solid 3 launched in the 2004 holiday season. It got squashed by the likes of GTA: San Andreas and Halo 2, along with a bunch of other things going on and other big game releases.

i know it didnt happen with GTA4 but its still common this gen