First I question exactly what the ability bonuses you came up with for Lizardfolk...a rough guess from default stats I see +2Str/+2Con/-2Int. A fairly standard array of bonuses.
Secondly, Skill points are listed in the Bestiary starting on page 306 based on creature type, Lizardfolk being a humanoid gives it 2+INT per HD.
You started with a 2nd level party...a 2nd level dwarf fighter with +2Con I only figure to have about 16HP ((d10 average of 5,+2Con,+1Favored) x 2 levels)...if he chooses the bonus HP for favored class per level. And the Lizardman fighter would average 19HP ((d8 average 4,+2Con) x 2) + d10 average 5,+2Con) so I don't see 19 vs. 16 being a distortion.
Skill pts would be Lizardman 6+(INTx3) vs. 4+(INTx2)for the dwarf so another slight advantage to Lizardman.
Base saves the Lizardman has another advantage with +4Fort racial (giving him +6 at 2nd level) vs. the Dwarf being a +3 Fort at 2nd.
The SQ of Hold Breath I would deem more than offset by the Dwarf's Darkvision,Defensive Training,and actually several others racial perks given to him. To the point of the Lizardman is short-changed here.
And of course the Lizardman will always be 1 class level behind the dwarf and actually unable to achieve a 20th level fighter.
IMO the Lizardman would be a good monster PC as it is very close to what a base race would have. As a player who seems to play Monster PC's often the Lizardfolk have always been an acceptable option.