When Metroid: Zero Mission for the Game Boy Advance was released on February 9, 2004, it was no secret that the original Metroid was included as an unlockable extra. Several months later on October 26, 2004 Metroid was released along with seven other NES games for the GBA in the Classic NES Series. People complained that buying the standalone version of Metroid was of little, if any value given that Zero Mission also contained the game and was not significantly more expensive. However, that turns out not to be the case.
There are differences between the standalone Metroid and the unlockable Metroid beyond the menu option that allows you to quit to Zero Mission in the latter. The real difference is in the graphics. This does not seem to be common knowledge, as I happened to stumble upon it when I was trying out games on my EverDrive GBA X5 (review forthcoming, be patient lads :) I have taken 16 screenshots of each version using Virtual Boy Advance-M to illustrate the differences. The images displayed below on the left are from Metroid Zero Mission, the images on the right are from Classic NES Metroid (reversed for mobile landscape view). Click on each image to give a 2x nearest-neighbor scale of the image :
The chief obstacle Nintendo had to deal with when porting NES games to the GBA is the difference in screen resolution. The NES can display 256x240 pixels, even though most TVs during its time cropped off a portion of each side by the monitor's enclosure. The GBA can only display 240x160 pixels, requiring some kind of graphics conversion. For the horizontal difference, all the GBA need do is not display the left and right most 8 pixels. Those pixels usually did not contain crucial details. In the mid-1980s, Nintendo game designers used a safe area of 224x192 pixels.
That leaves the vertical resolution. Many emulators of the day when these GBA ports were released would automatically crop off the top and bottom 8 pixels, giving 224 pixels. Nintendo did something close to this before converting the graphics, it appears they cropped to 212 pixels. Once those are gone, you still have a difference of 64 pixels between what the NES emulator in the cartridge is trying to display and what the GBA's screen can display.
The simplest way to handle this is to not display every 4th line. The NES draws everything with 8x8 tiles, so the tiles essentially become 8x6. This is what Nintendo seems to have done with Metroid on the GBA in Metroid: Zero Mission. All versions of Metroid: Zero Mission, US, Europe and Japan, all contain this version.
Also in 2004, Nintendo was releasing the Famicom Mini Series in Japan, starting on February 14, 2004. They released ten games in February, then ten more games on May 21 and a final ten games on August 10. Nintendo began releasing the NES Classic Series in the US, starting with eight games on June 7. 2004 and finishing with four games on October 26. Metroid was released in the third batch of the Famicom Mini Series (FDS version) and the second batch of the NES Classic Series.
It seems that during the months between the release of Metroid: Zero Mission and the release of the Famicom Mini Series Metroid, Nintendo took it upon themselves to alter the graphics tiles contained in the embedded Metroid ROM. The resulting tiles would look weird when displayed on a NES, but as close to ideal as possible on the shorter GBA screen. As a result, tile detail was improved across the board. Now Samus's head remains above her arm cannon and her face in the good endings has been restored. Kraid, Ridley and many of the enemies have better detail in their sprites. The background bubble tiles in Norfair now look complete instead of showing the obvious line deletions. Rinkya in Tourian look like circles instead of ovals. These improvements can be seen in both the Famicom Mini Series and NES Classic Series releases of Metroid. I would also note that there are some differences in the palette colors used in each version. Nintendo seems to have done something similar between the releases of Super Mario Bros. and Super Mario Bros. 2.
Therefore, the standalone release of Metroid in the NES Classics does have real value over the unlockable version in Metroid: Zero Mission. If you want to play Metroid on a true portable device (that is not a Nintendo 3DS), then the NES Classics release is worth picking up.