What is Superman's costume doing in a 20,000 year old ship?

When Jor-El jumped to retrieve the codex he stripped off his outer clothes and wore a black "activity suit". My impression was that the SuperSuit was a customised version of this design (notice that many of the Kryptonians did indeed have cloaks). As to whether it's more modern - that's difficult to answer without knowing the details of Krypton's fashion, there's no reason why it couldn't have been an amalgamation of Krypton/Earth styles.

As to how it appeared on a ship 18,000 years before Clark arrived on earth. Jor-El's consciousness ran the ship, given this was a seeding ship (and could so grow Kryptonians) it's not unreasonable to assume that it could clothe, feed and supply them too! My assumption was that the ship made the suit to Jor-El's specifications.

A comic was released before the movie in which it was shown that a member of house El (Kara El) was on that space ship which was sent to explore other worlds thousands of years ago but crashed due to damage taken by it during fight between Kara Zor-El and Dev-Em which also explains presence of skeletons of kryptonions whose cryogenic pods were shut down by Dev-Em.

http://www.ign.com/wikis/man-of-steel/Man_of_Steel_Prequel_Comic

I personally don't believe the ship created the suit....

After Jor-El's death, Lara places his clothes (including the family crest or 'S' symbol) in a display case that closes up...

I like to think the superman suit on the 18,000+ year old ship, was the clothing of one of the El family ancestors, that was part of the exploration into the stars and died in the process.

I think the suit was just the clothing at the time and was possibly placed into a display/storage case like Jor's was by Lara. Maybe Kryptonian ceremony of remembrance?

I believe the Consciousness of Jor-El simply 'presented' the suit to Kal rather than creating it.

This seemed better to me, as it shows how proud Jor-El is of Kal, to pass the suit down...and how the family crest of 'hope' would mean something worn on Kal...a badass protector of earth.

In the movie, Krypton, the invasion on earth, and the archive history all show a similar design in terms of costume. Many of them have cloaks, as well as symbols and runes prominently displayed. Being a colonial ship, the Kryptonian craft was shown to be highly developed in terms of provisions and functioning. Further, Jor-El's consciousness was the one controlling the ship. Thus, it can be fairly assumed that the suit was 'constructed' by the ship as per Jor-El's programming, which he then presented to Kal-El. It was Jor-El's key that contained all the coding and consciousness that gave the design to the suit.

It might just be an assumption, but since the Kryptonian technology gave out the idea of simple mechanisms and entities giving rise to complex implementations (the 3D faces or projections etc.) the ship created a suit as per the programmed instructions.

This also can provide the simple answer to why the suit perfectly fit Kal-El.

When Jor-El is talking to Kal-El in the ships control deck. Remember, the scene where he's explaining Kryptonian history in 2 minutes or less? He explains to Kal-El that several ships, "like this one" were sent out to explore the stars.

Kryptonian civilization has been around and intact for 1000s of years. The ship was a colonization ship from a time when they aspired to live among the stars beyond the bounds of Krypton.

I hope that answered your question.

Simple. Like Sirithil stated, but simply put; when Clark placed his key that came with to earth, inside the ship that was already there it uploaded Jor-El's AI and the AI had the ship to make the suit.

Jor-El's consciousness was uploaded into the ship's computer by Kal-El's command key. The AI-that-was-Jor-El used the ship's systems and resources to fabricate the suit while they were walking around talking, at which point he gave it to Kal-El. The ship was old but functional; Jor-El was not, neither was the AI based on his mind, and the suit was brand-new.

The reason why it has the costume is even weirder. See, one of you was right (for a bit). There were thousands of seed ships sent out, for exploration and colonisation. This is one of those ships; that's why it has the suite. It's a simple guess which blond niece of a certian alien is/was on the ship: Kara Zor-El aka Supergirl. Why it looks like a man suite - one size fits all spandex? It's all in the prequel comic for the Man of Steel movie.