Yeah, there's no real use for Altering Cave now the events have all moved on.
However, I personally like it as I always forget about it, and it has Kanto Fr/Lg music in it. That and the shock I got when I played LeafGreen and actually explored the Sevii Islands properly, only to find that Altering Cave first appeared there :D
The Space Centre's (Yeah, I'm correcting that spelling :P ) cool too, particularly in Emerald, where you get a double battle against Team Magma alongside Steven - especially as in Gen III you can read your partner's pokémon's summaries. Swampert and Steven's Skarmory make a brilliant combination, believe me :D
It also adds a little more depth to the game, and as Hoenn's tropical, and therefore nearer to the equator, it makes sense for there to be a space centre, as shuttles etc. are always launched as near to the equator as possible, in order to escape the Earth's gravity more easily.