If you think The End is tedious then you clearly haven't played the Metal Gear Ray boss fight in MGS2 on Extreme. I like the battle but it's essentially a test of endurance.
You have to take down 20 Rays, all with way more health than normal!
Act 3's opening is an awesome stealth scenario. At the time it was pretty unique for MGS and felt more like Splinter Cell (think Pandora Tomorrow's Jerusalem level) but on replays waiting for that guy is soooooo boring.
Peace Walker marks a huge departure from the original trilogy. It's rated T for teen, has a comic book presentation, the story takes place in small chunks to facilitate portable play, and there is no codec but rather tapes you can listen to. The bosses are unlike most of what you faced in the 3 MGS games too. And of course PW has a huge base management mechanic. It's way different.