Justice is Blind, and Autistic
Tbf Kojima probably understood that how heavily people leaned on the tranq gun and tried vary it up considering we have more nonlethal options in pretty much every game after 3.It's actually interesting you say that because I'd argue that MGS2 was the only one in the series that tried to discourage just tranquilizing everything, or at the very least asked you to weigh your options. If you left a guard unattended for too long, his CO will come on over the radio and ask why he's late for his status report. Eventually, he'll send a squad over to investigate. There were ways around it of course such as hiding the body and waiting for everyone to go away, but it wasn't just tranqing a guard and forgetting about him. Hell even the cheese method of just running out of the area and coming back to restart the CO's conversation required you to at least be aware of where you are and you had to be quick in leaving the area.
Outside of Twin Snakes, which was just MGS2's gameplay transplanted onto MGS1's levels, none of the sequels did this. So long as the conscious guards didn't stumble across the ones that fell asleep you were basically free to tranq everything. You are right though that MGS' stealth eventually gave way to just using the tranq gun on everything; it's actually a lot more fun not using it because it requires you to learn the level layout and take advantage of the game's mechanics.