There is quite a bit of stuff to learn I have to agree with tfwfh that the main problem can be the learning curve. Short sheets make it easier and then it is in the hands of the players. But lets look at some of your points.
- Automated damage rolls, or make eveything except special characters a mook
The only dice I roll at the table as a GC is damage dealt to players. All NPC's take 12 for anything including damage saves. Much easier to keep track of a number than to roll. Also this gives all the rolling duties to players. In fact players also use an active defense where they roll defense instead of having a static number.
- Stress and Subdual damage no longer require rolls but have HP totals. For example, 3 HP for one level of stress, 7 for two, 12 for three, 18 for four, 25 to knock out
You should check out Spycraft 2.0 for what was done with stress/subdual here.
Standard NPC's just take Stress/Subdual and I count it towards their damage save.
Special NPC's I again just let them take 12 on the required saving throw and note when the fail. So only players worry about making extra dice rolls here.
Maybe it is just my player's but it doesn't come up very often.
- Make fire, electrical, cold, etc damage types all just do damage (dangerous, I know)
I have a short sheet with the damage types listed out when a player has a different damage type it is up to them to tell me about other effects and it soon falls into a rhythm.
You can always cut out some of the secondary effects if you like or even rely on Action Dice to promote secondary effects.
Fire hits you, spend AD you now on Fire!
- Limiting feat choices to prevent huge collection of options
- Limited to only 2-3 abilities from your Race and specialty options
Limiting feat choice is a valid option, just be careful of where you make the cut.
Most of the time players will have one idea and will try to map it out with feat choices.
But the big problem can be dealt with by front-loading character creation. Have players think about where their character might go and then you'll see what feats might come up. Make short sheets for the feats. If you can attach it to the player's character sheet.
I would stay away from limiting Race/Talent/Specialties. They are all balanced against one another at 7 points and by choosing only some of the abilities you will find some options are just more powerful than others. Again a write them out for the player's then they are there ready to go.
- List of contacts for the PCs
I also pre roll treasure and fully write out all NPC abilities next to the stat block so I know what is coming up. I also don't allow 'Magic Shops' and unless players have the ability to craft magic items this cuts down on some clutter. Pre rolled prizes make things easier too.
If you are wanting to reduce some of the options you would be better off removing Race/Talents/Specialties, Classes (Base, Expert & Master), and feats (see note above) at character generation.
Since it seems most of the issues revolve around combat aspects you could also shorten the weapons/armour list. By having just dagger, shortsword and longsword you remove some of the options to help you streamline things again. Another place to remove extra options is with magic, remove spells you don't want or drop magic classes, also check out eh campaign qualities. Less options at the start less stuff to bog down during game.