Several Reasons: To begin with, a port has to be profitable and the pc market was't (and for some isn't) seen as massive as the consoles one, and there's certain genres (sports, driving, fighting, etc) that until recent years weren't so popular on pc (in companies' eyes).
About mgs the port was made by microsoft and the sequel by konami themselves, the first was an ok port and the later was awful. That's because in japan desktop pc aren't so common and games on pc are relegated to niches. Today ports aren't so bad performances-wise but lack of KB&M or settings (Ninja Gaiden, Shenmue 3, Asha in monster world). Things like judgment controversy shows that there's still resilience.
Sometimes ports aren't possible/profitable due to the game reliance on console(s) specific hw/sf. Ex: acording to kojima mgs4 wasn't on xbox 360 cause it was too big (ps3 had blu-ray) and ps3 emulator proves that it uses advance features from the ps3 processor. And like first answer if it's too complicated to port from console don't even bother ('cause it's too expensive/is going to be bad quality)
Some people (myself included) believes that the worst period was from like 2007-2008 to before steam started to being a common thing (2011 or 2012).
PS: HD collection was ported to 360 but development between consoles ≠ porting to pc and ms consoles market ≠ pc market. About metal gear 1 & 2, although konami, hudson, hal, etc, developed for msx, sharp and fm-towns it was a one-time thing (pc-88/98 games weren't action oriented and fell on the strategy, rpg, vn niche), this was already cemented by the time windows pcs overtook the market.