Before we get off on you bringing up the mechanical shortcomings and me agreeing with you but continuing to play anyway. Allow me to say yes, there are better mechanically designed games... we agree. Since gaming occurs with gamers who are people in real life, there are always conditions and gray areas. These conditions give modifiers to situations that might make one system more desirable than another.
If you have to judge it purely mechanically; then yes, Cortex leaves more than a bit to be desired.
Well, no need to read any further. Given the fact that there are good games, there is no reason to play bad ones.
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Of course you are not GMing, so play the game and have fun with your friends.
The first part of your statement is a value judgment and a false dichotomy. If the rule system made it unplayable then yes, there would be no reason to play it. The fact is that it's not unplayable (for my group), it is underdeveloped. Now we're back to what works with the group, and for my group it works... and there is the truth in the end of your reply.
If I had to run it, I'd probably use the Shatterzone or SR4 with some number crunched space rules.
The GM is in a rebellious mood because he feels constrained by the fact that most things in D&D have rules. He likes to run off the cuff, so Cortex works great for him because he gets to plaster over all of the holes in the rules and he's happy. I don't have to try to learn a lot of rules concurrent with D&D4e, so it works for me (and the other players).
Even though my writing style is not smiley, I have not developed a rhetorical vendetta against you.