SPOILERS ABOUT THE ENDING
I personally thought the ending felt lacking and tacked on. Kojima himself mentioned he wrote the games as they were made (proven by his retcon which changed Dr.Clark from a "he" to a "she") so he had the need to tie everything up here. Clearly, once he reached the end, he saw that the only way he could do that was by outright explaining everything to the player, something that could only be done with Big Boss, so he had to bring him back.
His sudden appearance makes little sense, even in the MGS world, and then he goes on to deliver a trademark MGS rambling speech. If that wasn't enough, Kojima then decided to use his favorite nonsensical plot point, FOXDIE. Oh fuck Big Boss caught it! He's gonna die. Wait, he's talking first. Talking. Talking. Oh he fell. He got up. He fell again. He's saluting. He's smoking a cigar. He's dying. He's dead. The stretching on of the scene sapped a lot of the underlying emotion. It just made little sense. Killing off Snake would've been better, that's the death the man created to be a soldier deserved. Not withering away for three months at home with Otacon as his housemaid.
The whole second half of the game felt pretty contrived and weird, mostly thanks to Kojima's struggle to wrap up all the plot points. It took away from the game. The (little) gameplay itself was spot on, and the Liquid Ocelot fight was perfect, but still... It didn't feel like the ending was deserving of the series grandeur.
MGS2 is still the best one, in my opinion.
SPOILERS