I think that at least part of the problem with these shots can be found with the original effects work. Take the vortex shot from Time's Squared. The vortex itself looks stunning, put apparently the SFX team that made the original shot decided to use the two footer for the flyby shot which 25 years later looks poor in close up in HD. The HD restoration is true to the original shot, maybe to a fault, but it still is a faithfull recomposition of the original work. I think the effects shots in the second season weren't as good to begin with as the first season effects.