I'm sure I'd be rating SO1 higher if I had played it before 2. But when a game is inferior in every way to a sequel and you play the sequel first, it kinda takes a hit or two.
Maybe... but even were this the case, I don't believe that means you can't award both games a high score. Take Mother for the NES as an example: while it's completely outclassed by EarthBound in every conceivable way, it's still a B+/A- game!
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http://www.youtube.com/watch?v=SBpfwpOPXNc&NR=1&feature=fvwp
I watch Planet Chasers Starlight Excellent all day, every day.