Actually, that's not completely true.
In the Japanese FR/LG/Emerald, there were e-cards to change the Pokemon in Altering Cave. There are normally only Zubat, but you could change it to Mareep, Aipom, Pineco, Shuckle, Teddiursa, Houndour, Stantler, or Smeargle.
However, the English versions of FR/LG/E have no e-cards for them, and they aren't even compatible with the e-reader in the first place.
The speculation was that we would be able to change the Pokemon in Altering Cave through Wonderspots. These are machines that you use Mystery Gift with, and they've been used at Pokemon Rocks America and the Pokemon Center in NYC to give out the Tickets for Deoxys and Lugia/Ho-oh.
However, there have been no Wonderspots for Altering Cave, and since these Pokemon are obtainable in Colosseum (through breeding) and in Emerald (Safari Zone, after you beat the E4), there's no need for them. I personally think that Nintendo had planned to release Wonderspots, but they were busy with the Deoxys promotion, and once that was done Colosseum was already out.