Maybe I am an idiot but some of it could have been easier to understand if the game didnt go all over the place with its script (ib4 2deep4u). I got some parts of it (Raiden thinking he was basicly Snake 2.0 for example) but it seemed that the game was trying to send 10 different messages with its story that just felt over convoluted to me (I also only played 2 recently for the first time and I played MGS1 in 1998, so my memory is a bit rusty for all those MGS1 direct comparisons).
Also I do prefer the gameplay in 1 since they still used a lot of stuff from the first that didnt work with other mechanics from 2 (areas with a lot of verticality are shit when its in a top down perspective, the leaning functions needed an entire controls overhaul to function properly as most of the times I ended up equipping/un-equipping my items).