GHEIST: Much more playable 5*s. A full stop (SOB+SOA)[Leviatonn].
Roots: A topend mono character (Gertjan). Almost all 7 power (unlike GHEIST who are likely playing several 6 power characters): makes them significantly less vulnerable to All Stars.
GHEIST don't have a compelling reason to go mono unlike Roots. Roots as also very cheap to put together, even the Cr (Noodile Cr) is affordable.
Roots does better currently in ELO. It often runs less 2*s and has a deeper roster of 3*s, making its draws more consistent than GHEIST. GHEIST has better "nuts" draws (Wardom, Bristone, Leviatonn) while Roots has only 2 "nuts" draw characters (Gertjan and Jeena).
Both tend to have a similar ceiling to their effectiveness in ELO as most of the popular clans have pretty good matchups against either GHEIST and Roots.