let's actually list the boss fights for the first three games and see how they stack up! (i haven't played 4)
MGS1
Revolver Ocelot - frustratingly meh running around in circles
M1 - just ok
Gray Fox - first boss fight that felt epic and the increasing difficulty was good
Psycho Mantis - great atmosphere fighting him for the first time but loses its appeal after that one time
Sniper Wolf 1 - same as above
Hind D - first time we see Snake actually stacked against really s**** odds and the challenge is fun especially when Liquid goes apes*** in the latter stage of the fight
Sniper Wolf 2 - better than the first but the limited options... limit the fun to be had
Vulcan Raven - good one that keeps you on your toes and the many ways presented to you make this one really fun
Metal Gear REX - epic, emotional, and certainly challenging so this one's alsoa goodie
Liquid Snake - melee combat on top of REX was a fun little thing but the car chase at the end can be frustrating
MGS2
Olga - solid pistol shootout with a couple of fun tricks you can use to your advantage and enough variety in Olga's pattern
Fatman - ridiculous setup but surprisingly fun with a great twist in the end
Harrier - same as the Hind D but even more of a challenge (f*** this fight in extreme, though)
Vamp - ok with enough thrills to keep your adrenaline pumping
Metal Gear RAYs - good stuff on normal, the most emotionally draining fight on extreme (which is also a good thing!)
Solidus Snake - i don't know why this doesn't get brought up as a positive in comments about MGS2's boss fights because this one's got the excitement, the epic quality, the accelerating pace, and the challenge that make for a good boss fight!
MGS3
Revolver Ocelot - best first boss fight
The Pain - ridiculously stupid yet also boring
The Fear - thankfully this one's better mainly because of the added variety to the ways you can beat him
The End - best
The Fury - hilariously fun and exhilirating fight
Col. Volgin - like the Fear fight, the number of silly little ways to beat him elevates tjhis into a good one
Shagohod - my least favorite of the robot fights but it certainly isn't bad
The Boss - second best to the End in terms of pure gameplay (but it sure is satisfying countering her CQC attacks) but certainly has the best atmosphere and the best end hands down
so yeah MGS3 still wins out with five good-amazing boss fights
2 and 1 have four each but 2 has the better four
--
all you need