Technical/Design Differences:
These original Time Fantasy characters are individually made full characters originally designed for traditional RPG-style games with a separate combat system (there's side-view battlers in an expansion for final-fantasy style combat if your game would use that).
The Elements characters on the other hand are made up of modular pieces that include four-directional animations (for in-world combat or actions). It has more flexibility for mix-and-match pieces as well as gameplay but that naturally makes it more complex to use.
Stylistic Differences:
Time Fantasy characters are slightly taller/bigger than the Elements characters.
By default the classic TF-style has a more muted and much "softer" color palette.
So using both character-styles together would clash.
But there's overlap for tiles: Both TF and TE character-styles use a 16x16 tile-base, so the tiles from both series can be mixed together and used with either character style: you just might need to do color matching for some older sets or add-ons that might be in one style or the other.
That should help you determine which set will be best suited for your project.
Thanks!