1) Scoring - I had to partially disappoint you. I am not sure how exactly scoring works in 1.2, but we had similar on Funserver 1.1 and it was good. You can fight hard with goon, that is true. But noob more often only waiting in base and sniping close aliens - result = camping, boring game for both teams and this noob camper have higest score. BTW, these noobs can camp in base whole hour.
But if noob want to kill acid tube, then he need to leave base and attack enemy base. That is harder and he can help other humans group or he atleast can feed aliens (good for them). Killing base is more valuable, because it is goal of the game.
2) Pounce, Tyrant - I agree, 1.1 is better.
3) Auto updates - sure.
4) Jetpack - Personally I think, that unlimited jetpacks are not problem, If there is not bad map. Anyway, there will be option for server owners and mappers, so they can choose between on/off/fuel.