They're about equal, but their playing style is quite different.
GHEIST rely more heavily on hard-hitting cards with higher risk but also higher reward. 2HKOs is usually the way to go.
Roots have a more balanced set of cards where you will usually win simply by increasing the life gap and not necessarily KOing your opponent. Rico, Noodile Cr, Gertjan and Yookie make up an extremely powerful half deck with only 12*.
*cough* *cough* Gertjan is support: card *cough* its useless on halfdeck *cough*
Roots has only kickass DR's and some good elo-banned characters, and some usable star-cheap cards.
Since this game is about eating opponent's face GHEIST wins as clan - Tho GHEIST has lower base power than Roots so you can use Roots to fight effectively GHEIST. Against everything else Mono GHEIST > Mono Roots.
In ELO, GHEIST but they are both hurting. You can make a fairly inexpensive Roots preset though.
Roots play better with other clans. They have characters that combine good base stats, SOA and DR which are very useful.
GHEIST is also probably easier to buy into than Roots for non ELO play.
Roots has solid 4 damage and many more 8 power characters than GHEIST.
GHEIST characters tend to threaten to do more damage and threaten 2HKO much easier than Roots.
Deeper topend 3* Roster (Yookie, Jeena, Noodile Cr Gertjan, vs. Leviatonn, Bristone and Dolly)
Better 5* outside of ELO (Kiki Cr, Shakra)
Better 5* ELO (Wardom)
Deeper topend 2* Roster (Arkn, Z340 D34d vs. Arno)
4* are fairly evenly matched (Ratanah, Gretchen, Tuck vs. Draheera, Toro, Methane)
For ELO, the choice is choosing between Gretchen, Jeena and Gertjan vs. Wardom and Leviatonn. Now that they've lost Draheera, the GHEIST roster looks very thin.