I liked CnC3. Then again it was the first CnC game I ever played, and I haven't yet had the time to finish Tiberian Sun, so maybe when I finish TibSun I'll change my mind.
But overall I feel where you are coming from. As a diehard Nod fanboy, I feel as if the first two games did the whole nod thing a whole lot better. The avatar was very un-nod, since it was a super powerful vehicle capable of going toe-to-toe with even mammoth tanks. The whole point of nod is that there is nothing in your arsenal that can win a direct fight with a mammoth tank, or a medium tank for that matter. So while GDI is slowly marching up with their powerful army, you're left to come up with a unique solution.
Nod's entire philosophy is to use high-risk, high-reward special weapons. Flame tanks/infantry, stealth tanks, and especially attack bikes could all do some major damage, but if the enemy defended properly or you messed up your micro, you'll just lose an expensive investment. This led to gameplay where Nod would win if they managed to continuously wreck things and make crazy plays, just like a terrorist organization, while GDI would win if they managed to keep control of the situation, pinpoint nod's weakness, and make one giant push to destroy them, just like a world peace and anti-terrorist organization.
CnC3 didn't have that. Both teams had pretty much the same units, and nod could win in straight-up fights because of units like the avatar. It was a fun game, but it didn't really feel like the same CnC from 1 & 2/