I think that Wailord and Relicanth are there as they where two of the pokemon around at that time. Perhaps Arsues(or however u spell it) hadnt created everything yet. Also, Relicanth is said to be 100 million years old and so would be there at the time, whales have also been around for many years. Also, the cave is deep underwater and whales can dive 10,000 feet below the waves, whilst relicanth lives on the sea floor and were the two most accsessible pokemon for the ancients or regis to use.
That's quite a good theory, actually.
Did someone take a bush (grass), some rocks(rock), a bucket of water(water), a lit candle(fire), some bits of a rusty stove(steel), and some cable plugs(electric) into a room and turn the lights out (dark

) and once the lights were turned back on stood a huge, powerful living being?
Rimshot.
Anyway, it's time for my contribution.
Regigigas, like most people have said, is from the Pangea time period. The reason it has Slow Start is because of its so-called eternal rest.
However, Dialga and Palkia have a lot to do with this.
Think about it - The two Pokemon control Time & Space. Dialga could have created Registeel ahead of time, while Palkia could have used its Space controlling powers to make Regice and Regirock at about the same time.
Then, after this was all done, Aruseus sealed Regigigas into his giant cave, and made the three Regis the keybearers to unlock Regigigas from his sleep.
Regigigas was probably more powerful than Aruseus back then, and 'Zeus would want King Regi under control.
Sure, I've basically said what a lot of others have said, but, still.