Listening to the comparison video, yes there are subtle differenses, no doubt, but I would have expected that for several reasons. The first, and most obvious is that the guy is playing presets live... his exact playing will never be the same each time, even if it's the same keys or melody... things like velocity and onset/duration/release of the keys will all have an influence on the percieved sound.
On top of this, there will most likely also be some component differences in the analog signal chain. The REV2 most likely do not use the same OpAmps, resistors, caps etc. and maybe even the curcuits of these has changed a bit, even if the functionality is the same as the original, and these small deviances will lead to slight changes in the tone between the two... they are both analog machines afterall.
But to decide weather one or the other sounds "better" is certainly a personal thing... you may be used to the original more, and find that better as a result... you may have the new one, and are used to it's tone, and find that better... not to mention the added polyphony and FX may make you prefer that one.
I really do not understand why anyone would even compare these two... if you like the first version better, then just get that one, it's even cheaper now than before the REV2 arrived. To be honest, I'm kind of tired of all these comparison video's between instruments, even more when they compare completely diffrerent synths, and always want f***** everything to sound like a MOOG... if you want the MOOG sound, go get a MOOG!