My hype list for the 2004 holiday season was Halo 2, Half Life 2, Metroid Prime 2, and MGS3. I was still several years away from finally getting past my aversion to GTA and the openworld/sandbox concept in general.
That's basically in descending order of hype. My hype for the first three was about the same, my hype for MGS3 was lagging way behind them. I wasn't pleased with the whole prequel thing, because I wanted to know what happened after MGS2. And then going so far back in time, 50 years into the past, that just felt like adding insult to injury. A big part of the appeal of MGS for me was that it was high tech and mildly futuristic.
Anyway, blah blah blah. Point is, after the holiday season dust settled, MGS3 ended up being the one game out of all of them that really grabbed me and just wouldn't let go, became a bit of an obsession for a while, god only knows how many times I replayed it, not to mention MGOnline. Eventually I did get into GTA and I played all of them including San Andreas. I liked it, but it didn't strike me as anything special. No doubt it was bigger, but some times it felt too big. It had a ton of different shit to do, but IMO a lot of it was a stupid waste of time. I liked it but thought it was severely overrated by rabid fanboys.
So, yes, I'd still give it to MGS3.