Early Footage

All of these images were taken from places like GameTrailers.com, 1UP, GameSpot, IGN, and other places.

Screenshots

Pretty much the entire area was changed here, with the area looking more like a jungle instead of a forest. There also appears to be a slightly elevated path above the ground, possibly the unused bridge, but there isn’t enough of it to see to get a solid verification.

The long helicopter was replaced with a round helicopter in the final. They also let you fight the helicopter from the higher raft, instead of forcing you to the bottom one for it to appear. The background is also slightly different.

Those vehicles only appear in Mission 2, and only piloted by the soldiers in bandanas. Note the background, which is either starkly different, or repositioned and recoloured.

Those boxes aren’t there in the final, nor is that ring on the left.

The background was lower in the prerelease, and there isn’t supposed to be a prisoner there. There are prisoners up ahead, but there’s no way you’d be able to get them down there.

There’s never that many octopi in that area at once, nor do they ever go in that direction.

Robot is firing a rocket, the bazookas have no “patches” (so they’re brown instead of grey) and there are no objects or enemies on the floor below in the final, it’s empty. Plus, at that specific area there’s a tank, no robot or bazooka Joes.

The entire room was altered for the final, changing it to some ruins and adding a few corpses. The only change to the Black Hound (not pictured) was the changing of the blue on it’s turret gun to white. The HUD appears to be in Metal Slug 4 style, with that bar always there. The score for both players is “123456”, most likely filler until they worked on it.
Enomosiki supplied me with an alternate version of the screenshot, with none of the text, but the quality was lessened. I'm highly confused about the green background, compared to the original's red/brown.

You can’t see it very well in the image, but there appears to be a small jellyfish in the glass. The final has it replaced with dozens of those Rebel Armour things. The brick tiles also seem to be different between the image and the final game. The scholar is also shifted to the right in the final a little.
That middle image was obtained from some Yahoo! Group, and it appears to be the same as the one I took from the game, sans the scholar's position.

This looks a little like the harbour area of Mission 4, but it doesn’t appear in the level. That background is used, and I believe that design is slightly similar to the section after you get the Drop Shot, but it’s rather different. I may be wrong, but I’ve a feeling that metal walkway there is used in Metal Slug Advance, but I’m not definite.

That hover jet thing doesn’t appear anywhere else other than Mission 2 and unused levels. The bazooka is also missing it’s patches, resulting in it being brown and not grey.

The background is different (the image has enemy robots and control panels, while the final is used in MS3's third mission's factory area), the floors seem different, and unless it's yet another colour problem that the other pictures Enomosiki supplied me with have, the background is differently coloured.

Another image from Enomosiki, this shows that this area had the entrance before where you start in the final. However, unlike the appearance of this area in one of the videos, this uses the same background as the previous image, the Slug Gunner and it's work thing is placed back, and the officer doesn't seem to be there in the video. And judging from the score, it all seems like a mock-up.

Yet another image sent in by Enomosiki, this shows those two weird tanks and some gasmask soldiers fighting Eri where the Slug Gunner and a work station are placed in the final. A battle takes place here in one of the videos, although it's only robots in that fight, no soldiers.

The tank on the left features a much simpler barrel than its final sprite. Thanks to Ivo for pointing this out!

And Enomosiki drops another image on my back. No officer is ever present during that area, a helicopter doesn't appear until further on, and no helicopter ever uses that gun. Note Marco's 02 lives, and the energy bar being there.

Image from Enomosiki. The cultist guy is green (I've only seen him purple, but I seem to recall him being different colours at that point), and he never floats that high. Those bandana guys don't come in until you've cleared all of the robots out and move to the right. Plus, no brown ones with those arms are never fought there (grey ones with those arms are, though), and what's that white thing near the cultist?

VIDEO 1

Now we’re onto the videos. The first change we see here is how that bush flashes orange when shot, just like enemy vehicles and whatnot. In the final, there is no flashing, only shaking.

Rumi drops an unused item, that little pork-like thing.

Nor do I know what this is. I hate these low-quality Quicktime files, they make me post stuff that may not actually be unused. =(

The camera doesn’t go down that low until you defeat the helicopter.

In the video, the helicopter shoots all three bullets almost at once, but in the final there’s a slight pause between them, allowing you to slip through them. Plus, it seems to shoot more frequently.

And when the helicopter is defeated, it explodes in an X style here, but hurdles downwards and explodes in a regular fashion in the game.

The natives don’t appear until you reach the ruins blocking your way.

That bush isn’t there in the game.

The ruins that block your path aren’t there in the video.

VIDEO 2

In the final that top stair is slightly different: In the video there, it’s a normal stair, but in the game it’s a block covering a stair going downwards.

You’re given a Dual Machine Gun in the game, not a Rocket Launcher.

Marco receives an unused item, the laughing skull. I think it comes out of that little pink worm in the video, and not a hot spot on the wall. Odd.

In the game you can dander on through to the top path, but in the video you’d have to deal with a shaman generator first. Marco chooses the bottom path, instead.

Strangely, when Marco goes through the bottom path, he ends up in the area that leads to the boss and the Black Hound (1: 4 3_4), instead of the area with the Slug Gunner (1: A 3_A).
Anyway, here, the top two stairs are average in length, while the one below is longer. In the game, the top stair is of average length, the second is very long, and the third is ridiculously short.

Although Marco takes the path that would lead him to the boss, he instead winds up in a severely different version of 1: 8 3_8! There’s too many differences to list, so I made a really, really crappy map of it. Click here for map!
It’s also worth pointing out that the shaman generator doesn’t have explosions when it’s fractured or destroyed in the video, it just suddenly has heavy damage and disappears just as suddenly.

VIDEO 3

The only difference I’ve noticed here is that there’s a large tree in the background, but in the game it’s only small, thin, feeble trees.

VIDEO 4

Marco destroys that truck there, but the soldiers standing on it’s lifty-uppy thing don’t fall down until the actual thing explodes, despite the fact it’s retracted down, leaving them floating there. In the game, the normal laws of gravity apply.

In the game there’s a soldier waiting in that vent.

VIDEO 5

Marco ends up at 3: 4 1_3, the area before the boss, instead of 3: 6 1_5. Interestingly, there’s a little part before where you start in the game, showing a glass window and three robots activating...

And the middle one (who activates and starts moving first) goes over to the right wall/door, and does THIS. I’m not sure what exactly it’s doing, and if it’s actually doing anything and that’s just something in the background. I think it’s either…

The robot doing that “go go go” motion that typical army sergeants do.
The robot operating at something.
Or a door rising and lowering repeatedly.

But either way, it’s kinda weird, yo.

There’s also one of those little workplace things, featuring a sweaty workman and a Slug Gunner. It’s not in the game, as it’s in 3: 6 1_5.

There’s a trio of shield soldiers accompanying the robot in the game, but it’s alone here. It’s also a regular type in the game, not that one with the bigger hands.

VIDEO 6

There’s a Metal Slug there, but in the game there’s a Slug Gunner here, as with how the previous area in the video had one.

Intriguingly, the game has brief appearances from the shaman and an officer here, but in the video the officer appears to sic four robots on Marco.

After that, there’s a scholar, who rewards Marco with some gas. In the game there is no scholar there, and the soldier above simply mans an alarm.

Marco destroys the tank, resulting in it’s shattered frame remaining and leaving an Armour Piercer, which would be useful is Marco hadn’t lost it earlier. In the game, the tank completely explodes, leaving no evidence of it being there, nor an Armour Piercer, since the Slug Gunner doesn’t use those.

The second tank leaves a Heavy Machine Gun, but leaves some gas in the game.

That scholar isn’t in that area in the game.

Marco encounters three Girida-Os here, but faces the wrath of an officer sending three robots and two trucks against him in the game.