I do love MGS 3, I believe it's a brilliant and well crafted game that is one of the top games within the PS2 era. However, I see Sons of Liberty to be that much better than it in many aspects.
Gameplay wise, MGS 3 felt a lot more fluent and more like MGS 4 to me, and we all know that it was really easy to finish MGS 4 on "The Boss Extreme" difficulty, thus making MGS 3 very easy to finish on "European Extreme," with the added incentive that it was game over if you were spotted in MGS 3.
MGS 2 on the other hand is a whole different story. The gameplay is very clunky and very frustrating at times, but once you get around that, it feels a lot better. It was also an extreme challange because the difficulty ramp in MGS 2 skyrocket's throughout the game. Plus it makes it so much harder considering the fact that you do not have camo and must hide using your own wits, and not just keeping still half the time. Especially in "European Extreme" was damn near impossible but pushing on enough, you could do it. Took me a good few months to do.
We all know Metal Gear Solid for it's very in-depth storyline. No matter what game you play in the series, you know that your going to be confused at least once. So many terms to know, nanomachines, FOXDIE, EPS and all those other terms you never really understood until later in the game, or in another game perhaps.
Metal Gear Solid 3's storyline is by no mean bad. In fact it's really good as it basically is the starting point for the Metal Gear series (The older versions can wait for another day, but chronologically it goes 3, 1, 2, 4) as you play as Big Boss, who will later become the father/brother of one Solid Snake. The "Snake Eater" mission is what you play through, which is good because it sets up Big Bosses character for the rest of the series, although you don't see much of him, but you hear a bit about him.
Metal Gear Solid 2's storyline, for me, triumphs over the MGS 3 story. It's not just the fact that Raiden is in it, cause he was slightly annoying I must admit and you could just feel that he was very pitiful for someone who was so badass at the end of the game, and in MGS 4 as well. Snake's part in the MGS 2 story is what gets me. While you only use him during the "Tanker Incident" and see Liquid hijacking "Metal Gear Ray," you get this feeling that it's not over, and your right as you will have to face him in MGS 4. But MGS 2 does the brilliant job of setting everything up for anything that comes after it (AKA Metal Gear Solid 4). More importantly it sets up all the characters within, even if they died or you thought they were dead (Vamp, looking at you.) The whole story sets up Metal Gear Solid 4 perfectly and explains more into the "Shadow Moses Incident" and other various points of interest that you wanted to know.
I know that this is a very long... 'Rant' I suppose, but I did want to convey my reasoning. I won't make this any longer now, but I am a strong fan of this series and while most people like MGS 3 over 2, I am one of the very few who prefer 2 over 3.