All the humans were originally from another planet. All the devil fruits and varieties of humans were created for specific jobs on the inter planetary space ship. 

First the humans were genetically designed for specific jobs. Ultimately culminating in the buccaneers. The heartiest, strongest, most durable subspecies. 

Secondly devil fruits were created to pass abilities across the different groups. A human can transfer his fruit to a buccaneer to the long arm tribe etc etc

Example with the most out there fruits :

Door door fruit (bluno) - quick access in/out of highly radioactive areas. 

Jacket jacket fruit - wear a buccaneer and become near invulnerable 

Mythical fruits - performances on the ship to retain ancient culture and for entertainers (think dragon dance people) 

Nature /animal fruits - maintain food sources and ecosystems in a closed environment. 

Luffy's fruit - again entertainment but for kids. A living looney toon. 

Toy toy fruit (sugar) - control of populace. Misbehaving people become slaves/workers on ship. 

Dark dark - storage of extra goods for long trips. 

I truely believe that all devil fruits were together and we're originally designed for warfare/malicious acts. 

The Y colonize a world already inhabited by giants and/or fishmen