The difference is that you did it before. You knew what to expect, but when you first play it, that sequence comes out of nowhere and the game does nothing to prepare you for it. There is exactly one warthog jump you have to do before this, and it's almost at the very start of the game. Suddenly the game expects the player to be able to execute precise maneuvers on a timer after a whole game of casually doing donuts in huge open spaces.
I think there's a whole lot of luck involved in making your first experience with that section enjoyable. Eventually I learned how to have fun with it, but at first it was insanely frustrating.
I think that adds to the urgency and epicness of the final sequence. The build up to the Warthog rush, the music during, and mowing through droves of enemies like never before makes for great gameplay. From a game design perspective, it isn't conducive to success. But from a harder to quantify "experience" point of view, it's absolutely exhilarating.
"Wildcat destabilization? Girl you cray. What do you mean "blow up?" So I just have to go out this door and up this elevator and then end game cutscene, right? Oh, how convenient, a Warthog for me to ride into the sunset on. Hm, I don't remember the ship being this complicated. Pretty maze like, go figure. You want me to jump over THAT gap. Fuck outta here--okay okay, only two minutes or we're blown to shit, I get it. Foehammer, noooooooo. Oh shit oh shit oh shit. Shit is real, how do you turn this beast?! Fuck, the Flood. Oh, I can run them over? Why didn't I do this before? Haha, this is fun. OH snap, I flipped the Warthog over because I WAS NOT PREPARED FOR THIS SHIT. X-X-X-X-X, flip the fuck upright, dammit!"
Most people died there, I assume.