The biggest reason I see GDI struggle against NOD is because GDI has no anti-infantry infantry, at least until level 12. Especially considering the NOD Cyborg and confessor are tier 4 infantry units that most player get early, and why I especially thing cyborgs are so strong vs GDI. With flame troopers and flame tanks to easily counter standard infantry, cyborgs become too strong for GDI, with only vehicles (ground or air) providing any serious counter to infantry.
That's just what I've noticed playing either side. As NOD, get out cyborgs and flame troopers/tanks, or cyborgs and confessors, and keep them paired up. Cyborg handles any vehicle, other things handles infantry.