The Trident is the overall better design with a higher performance ceiling.
Flying gantries are a solution forever in search of a problem. They can work okay and they're fine at the speeds that were common when the V2 was first designed, but there's a reason why the community has converged on fixed gantry designs. They're neat to watch operate but they don't offer any practical advantage. The V2 tends to be relatively slow by modern standards, especially in terms of accel.
The Trident isn't without flaws but it's a perfectly fine starting point and the huge community does mean that most of the bigger design issues either already have a usermod or somebody working on cooking something up.