Yeah, I was also disappointed almost immediately once I started playing Twin Snakes. It could have been a great game if improving the graphics was all they (Silicon Knights) did, but they made some weird changes and decisions with this one.
*They made Snake a ninja capable of feats that almost rival Neo from the first Matrix. This also relates directly with the overdirected cutscenes, which were too much like a bad action movie.
*They re-recorded all the dialogue. Most of the same cast from the original MGS reprised their roles, but they didn't sound into it, like they were phoning it in. They dropped Mei Ling's cute accent too.
*They changed certain lines of dialogue. One example would be Otacon's prideful remark about his Metal Gear design. In the original MGS, he says "I like to think of it as a character flaw" when speaking of an odd flaw in his Rex design (from what I remember), but in Twin Snakes he says "I like to think of it as a design flaw". That change totally takes away a part of his character and his obsessive fondness with his metal gear desgn.
*Arguably including the first-person firing mechanic from MGS2 breaks some of the boss battles and makes the combat in the game less interesting.
What a shame. Those are my complaints.