As for Skies Of Arcadia, I believe the original is more difficult because I couldn't grind as much as I wanted to in the original compared to the remake. This puts a damper on my money-making efforts, which extends to my usual habit of collecting every weapon in my inventory considering how I play RPGs. Quest-wise, they are about the same since certain quests were removed from the original to the remake and fitted with a few new ones. Depends on what you think is good or bad. In this case, I definitely prefer Skies Of Arcadia on the Dreamcast considering that Pinta's Quest on the VMU is a pretty cool mini-game which does supplement the income.
As for picking either or both versions, there's definitely some bragging rights to owning the original but then again, there are some fun added-content found on the remake of certain games. Bionic Commando: Re-Armed and Strider HD, in my opinion, are worth picking up. Kingdom Hearts HD I.5 Remix does give you the Final Mix version of the game, which was exclusive-only to Japan, from what I heard. I was also a fan of the original Flashback: Quest For Identity but I heard the remake is horrible.
Sorry for rambling... Hope you enjoy whichever choice you make.