Most surprising discovery/secret/unlock/experience in this game?

[MGWSpike]

Blowing up the Hind replaces them with hovering platforms when you go to the cliffs - Freedom Fighters influenced?

Here's one I only noticed as recently as Master Collection:  LBJ's voice changes.  Although only one actor is credited, he sounds much more haggard in the finale than he did in the initial phone call with Kruschev.  Perhaps a deliberate means of illustrating how crises like The Boss's defection can take a toll on political leaders?

The hovering platforms are based on prototypes from the 1960s.

I have a theory about the Lyndon B. Johnson voice change. Originally it was the CIA Director who'd award Snake with the medal (source). They changed it afterwards but probably didn't bother re-recording the few lines for the US dub. The CIA Director is credited with a voice actor but he has no lines at all in Snake Eater (he just lets out "Mmmph" when Big Boss passes by him without shaking his hand).

Anyway, it's hard to single out one element that is most surprising about this game and other members already gave great answers to the question, so here are a few additional stuff you may not know:
- Snakes runs slower when moving in the mountain part of the game. Moving around while wearing a cardboard box fixes this.
- If you use the Binoculars to zoom on a target, then quicky switches to a pistol, Snake will precisely aim at said target. Therefore you can easily turn any pistol into a sniper rifle.
- You can get a full length life bar before the Ocelot boss fight. Just repeatedly run into a spiked trap, half heal Snake, wear the DPM camo, wait. Rinse and repeat.
- You can quickly defeat The Fury using only... the knife. It's risky but it makes quick work out of him (3 knife combos and he's done).
- When under the effect of a stun grenade, The Fear will see his stamina bar take damage if you use a lethal weapon (i.e. an AK) against him.
- The ending of the game was strongly inspired by the opening of The Rock. People usually know about the influence of this film on MGS1-2 but I rarely see it mentioned about MGS3.