The Series II has more hp and torque, but it delivers that power at a higher RPM which is SLIGHTLY less desireable.....not enough to keep me away if I wanted to upgrade!
Series 1 varied by year, as well. 92 was the beginning, 93 was slightly improved (different heads and slightly different valvetrain), then 94 and 95 were identical. The Series II has ALOT more aftermarket mod support, though. The Series II has a bigger supercharger, but it spins slower to produce the same flow, although the indicated boost with stock pulleys is lower (inconsequential.....it'* the flow rate that really matters). This can be overcome in both Series with a smaller SC pulley for more flow and boost, but the M62 has to spin faster to accomplish this.
97 was the first year for the new transmission in the Series II, but there are thoughts that the older 4T60 series had fewer problems, despite it'* age. Again, though, the 60 series has less aftermarket support than the 65.
What it would boil down to for me, if I were looking for a different SSEi, I would look for Series II if it was in the budget, otherwise, I'm quite happy with my Series 1, and it does have alot of potential. They're all tough as hell