In my game, I allow the players a choice. They can have the 2 one point bonuses or they get a one point bonus and one of the following:
* One trained skill.
or
* One talent.
or
* One extra HD.
I decided on skill instead of a feat (granting a new skill) because in a 20 level progression, the players will already get 16/17 feats, and they don't get a lot of skills in comparison. Also, it keeps them from having to spend a feat on a new skill unless they just want to pick up a lot of skills. Just one skill though seems underpowered, so I was thinking of maybe two class skills or one non-class skill.
Talents are plentiful enough but this allows them to pick up an extra if they really need it .
The HD is an option I just thought of. Yes, 1st level starts off with a bunch of HP, but since this doesn't come in until the 4th levels, it allows those that have since fallen short of HP to make up for it somewhat.