Metal Gear is one of the MSX Konami games that got ported quickly and cheaply for cash-in purposes. It really shows but it's not as bad as people make it up to be. It is quite good despite the original ver. being superior. Kojima was just an employee of Konami and of course he would have no say about porting his game, no one would kiss his ass like they do today.
The one that really gets the undeserved hate however is Snake's Revenge. It mostly comes from stuff like:
1. Kojima didn't work on it: Kojima was just another designer at Konami, not a superstar, and he had his hands full with other PC88 games like Snatcher. The team responsible for Snake's Revenge was the same (or mostly) the Castlevania team if I'm not mistaken. And it wasn't just a cash grab like the port of the first one.
2. The side scrolling stages!!!: It's only a portion of the game and it's not bad, it's just mediocre.
3. It's not the official sequel!!! Metal Gear 2 Solid Snake is!!!: This game convinced Kojima to do the "actual sequel" not because it was shitty however.
SNAKE'S REVENGE might not be a "official sequel" but really who cares besides hipsters and AVGN watchers. It is a solid game all around. Not saying that a PC Engine version of MG2 wouldn't be nice...