I think there are three key issues that need to be tackled regarding the Rule set.
1-Rework SPECIAL and Derived stats. Remove at LEAST special bobbleheads.
2-Revise Skill system. This includes determining caps, skill points per level, available points and usefulness of skills.
3-Revise leveling and Perk system. Heighten the cap, or make it harder to reach. Make perks more meaningful.
#1- Each SPECIAL stat needs to have significant meaning. Honestly I feel like I could get by with a 1 on all my stats. Part of this problem is the derived stat formulas.
You simply start with too much free carry weight, health, action points, skill points per level. Lower these so they are derived more linearly from SPECIAL.The biggest losers in SPECIAL are Perception, END, and CHA, but they all need work. Perception REALLY should be tied to effective range of weapons. CHA is going to be hard to figure out, I kinda felt that it wasn't that important in Fallout 1 and 2 either. Bobble heads for special need to be removed, I don't like feeling gimped or building my character based on something like this. You can keep stat boost in, like bioenhancers for "THOSE", but make them very rare.
Side note: Also, making the numbers for Health and action points proportionately larger doesn't make them better, it makes them WORSE. It unnecessarily complicates the system.
The problem is, some attributes grant better bonuses than others, namely carry weight(STR), action points(AGI), critical chance (LUCK), and skill points(INT)... These are the priority attributes... the others are just to flavor. A player should have as much motivation to put his CHA at 9 and his INT at 1 as he does to put CHA1 INT9....
There has to be some form of opportunity cost, based on how you want to play the game.
Bottom line:Make all stats meaningful, fix derived stats. Lower skill points given.
#2- Revise the skill system. I think they've made a step in the right direction with combining some skills, but they didn't balance the way to master them. Either change the skill cap and skill checks, or rework distribution of skill points. I personally like them being balanced around 100, and as much fun as it was getting your first aid skill to 300, it was pointless! Make each skill at least potentially useful! Barter was trash, I was rolling in caps EVERY game. This brings us back to Tag skills. If they are balanced around 100, getting twice the skill points for tagged skills is ridiculous. This is where my system of bonus perks for tagged skills come in, lending a unique flavor to each character, and lending reason to tagging skills aside from a one time bonus. Mastering 5 skills should be HARD or IMPOSSIBLE unless you take a lot of skill perks. I think being a generalist character SHOULD be an option, but it shouldn't be so powerful. It seemed every character I made simply ended up the same because of necessity of certain skills. I maybe took a few novelty perks to make my character feel specialized, but the min/maxer inside of me hated it.
See http://www.gamesas.com/bgsforums/index.php?showtopic=960703 for original thread.
This system essentially means characters get certain bonuses to their tagged skills at 25,50,75,100 a la oblivion. I know people hate "making this more like oblivion", but its a stronger combination than the current system. Keep in mind ONLY Your tagged skills get these bonuses, and I thought it was an interesting system, is something BETHESDA is comfortable with, and can really help make Tags important, while giving some of those under powered, but well thought out perks a home. IE Infiltrator perk at Lockpick 50. Also... Bring back outdoorsman =)!
Bottom line: Make all skills useful, and make them a little more character defining. It shouldn't be easy to master multiple skills. Make TAG skills mean something.
#3 Revise leveling system and perks. Remove or heighten the level cap, and make it difficult to get there. No brainer. I also think perks should be lowered to once every 2 levels if NOT 3. While it was fun picking perks every level, there just weren't enough useful ones to go around, and it felt mundane after a while. Put a LOT of thought into each perk, make some difficult to get, requirement wise. You should NEVER be able to get every useful perk in one, or even 2 playthroughs. There were some perks like "contract killer," that brought some interesting ideas, but were ultimately underpowered. If it opened a unique quest chain with the Talon Company with interesting rewards, and had some other bonuses, etc. it could have been good. There some good ideas out there, but they lack proper implementation. If all perks are equal, some will get left in the dust by the role the character is playing, but THATS THE POINT!
Bottom line: Make reaching the level cap feel like an accomplishment. Make non-combat perks more applicable, and make all perks of similar levels equally balanced. BECAUSE bethesda threw "traits," (which by definition help define a character) into the perks, they need to make the perks more character defining by use of requirements and usefulness.