I remember reading somewhere (probably just a rumor) that they lost the original code for PDS.
I thought Panzer Dragoon Saga kind of wasn't as great as its reputation makes it out to be :S The story and atmosphere and visuals are all amazing but the dungeon designs are sort of lacking and the battle system... wastes a lot of time without really being challenging -- stuff like hanging out in the enemy's blindspot forever till it becomes vulnerable.
A full on remake could fix that though.
Honestly I'm reading this more as MAYBE Sega bought Atlus more because they want to use them for localizing Sega things than creating entirely new Shining Force games or whatever.
... Also i feel like a 3D remake of Dragon Force for the 3DS would be... rather appropriate and probably a good use of the 3D effects. Give M2 some more work :D