Merric, I'm saddened to hear you don't like the CORTEX system presented in the rules. Me and mine group seemed to really like it a lot.
Can you express what it is about the rules you don't like? I'm just curious if there's something our group has overlooked that you're having issues with.
I don't like the resolution system.
Most systems I play use a die roll + mods; which basically translates to having a basic level of competence and then you exceed that level by some amount. Serenity doesn't have that basic level: instead you gain the potential for greater success, but your poor result doesn't change very much as you become more skilled.
So, this is quite different to how the games I normally use work. This is not, in itself, a problem. Indeed, my first reaction to the Serenity system was "Ooh, cool!"
However, in the two sessions I've played, it turned out that the system was extremely swingy in the rolls you'd make. This turned out to be a big problem in combat, where a good attack roll vs a bad defense roll would turn into a lot of damage. In "Billy", Billy was meant to join the PCs for a short time and help them, but the trigger-happy idiots tried shooting him in the leg rather than talking. So, Billy shot back - 2d12 skill, rolled near a 20. Nash rolls about a 3... oh dear. As the difference adds to the damage (4+8 wounds, 9 shock in this case), even story points are having a hard time keeping Nash alive.
(I'd like to say that the players have learnt their lesson and so won't be bringing out the guns soon, but I don't think they have. Take note, boys and girls: Guns kill PCs in this system!)
However, this swinginess of the system concerns me. I know that people like Cam who are well-versed in the system only roll dice for the important stuff, which is excellent advice. I'm not quite sure if I can prise away the dice from my players - and my reactions. "You're doing that? Cool - roll for it!"
What doesn't help is that I've also recently gotten hold of the new Doctor Who RPG (my review), which is quite similar in a lot of ways to the Cortex system whilst actually being quite distinct.
Resolution is 2d6 + Attribute score (1-6) + Skill score (1-6) vs target number; converting a Cortex character would just involve moving the Attribute or Skill from a die code to a number - so d2 -> 1, d4->2, d12->6, d12+d2->7, etc.
And it has "Story Points" rather than "Plot Points", but the way they work is different: either they give a bonus to the roll (before you know the result) or they change the level of success: so you can spend points to move from Major Failure -> Failure -> Minor Failure -> Minor Success. (The levels of "Success" and "Major Success" can't be reached by story point use after the roll) Or you can go the other way - which helps a lot to survive combat.
(The failure/success levels are based on how well you rolled. Roll 8 under the target, Major Failure. Roll 8 above, Major success).
Of course, I haven't gotten to use the Dr Who system yet, so it might turn out to be as irritating as Serenity's.

Cheers!