Regarding the favored class bonuses of +1 hp or +1 skill rank, this was one of the first things I overruled. I said simply that PCs get both whenever they level up in their primary classes.
Here's my reasoning.
1) This greatly simplifies the accounting process with skill ranks. If as DM you are double-checking your player's number of ranks spent, they could legally be over the expected limit (including Int and racial bonuses) by as much as their PC's character level and there isn't a way to mathematically verify their math is correct, because there is no way to verify that bonus hp have been properly added in so long as the PC's hp total is less than maximum hp possible for that PC.
2) The matter of getting an extra hit point for a 'skill-based' character--up to 20 extra for a 20th level character--is not a big deal. My philosophy on characters with lots of hit points is that they make encounters last longer and make them more interesting; they let players enjoy their nifty tricks more often and last longer against more bad guys. If this extra hp goes both ways (for monsters as well) then the DM gets to bring to bear more of the monster's specific strengths & tricks themselves; versus picking out a monster with a broad array of spell-like abilities and maybe a customized list of class spells, only to see that monster toppled (or help execute a TPK) in only two or three rounds' worth of actions.
3) The matter of getting an extra skill rank for a 'beefy' character isn't a big deal either. I think that the built-in limit of character level as your max ranks for a given skill keeps bonus SP from being used effectively as a power-gaming tool.
Here's my reasoning.
1) This greatly simplifies the accounting process with skill ranks. If as DM you are double-checking your player's number of ranks spent, they could legally be over the expected limit (including Int and racial bonuses) by as much as their PC's character level and there isn't a way to mathematically verify their math is correct, because there is no way to verify that bonus hp have been properly added in so long as the PC's hp total is less than maximum hp possible for that PC.
2) The matter of getting an extra hit point for a 'skill-based' character--up to 20 extra for a 20th level character--is not a big deal. My philosophy on characters with lots of hit points is that they make encounters last longer and make them more interesting; they let players enjoy their nifty tricks more often and last longer against more bad guys. If this extra hp goes both ways (for monsters as well) then the DM gets to bring to bear more of the monster's specific strengths & tricks themselves; versus picking out a monster with a broad array of spell-like abilities and maybe a customized list of class spells, only to see that monster toppled (or help execute a TPK) in only two or three rounds' worth of actions.
3) The matter of getting an extra skill rank for a 'beefy' character isn't a big deal either. I think that the built-in limit of character level as your max ranks for a given skill keeps bonus SP from being used effectively as a power-gaming tool.