One factor that might make a difference is whether you prefer a closely miked recording or one with more space. The Martin Pearlman recordings evoke a large hall, while the Trevor Pinnock recordings sound closer and more intimate.
I like the performances and the close miking on the Pinnock recordings, but the sound is good, not great. It was recorded in the early days of digital. It would be great if they would rerecord it with 24 bit technology.
Has anyone heard the Apollo's Fire version?