Half-Elf: I'm a little concerned that +2 Charisma without penalty might be a bit too good and would naturally force any player into playing either a Sorcerer or Bard into playing a Half-Elf instead. However at the same time, charisma is the least powerful (and most powerful) stat in the game. Also, with all the bonus skill points, Half-Elves might be too good at being skill monkeys.
I would shy away from a bonus to Cha for half elves without a penalty unless you simply removed the penalty from other races. I don't think you need
a penalty to offset a bonus (because the penalty doesn't make the race weaker, it just limits its options), but I think all standard races should be the same in this regard. So I'd say penalties for all or penalties for none.
Half-Orc: I feel more comfortable about these guys. I've seen alot of guides write, "Why be Half-Orc when there's Water Orcs?" True, so in comparison to them, I felt that giving a +2 on strength checks would allow a Half-Orc to compete when using maneuvers such as grapple, trip, or bull rush compared to a Water Orc's higher strength and damage. I included a +3 racial bonus to Intimidate to overcome the -2 to charisma so they could receive an overall bonus of +2.
In my own personal fix, I moved the -2 penalty to Int with no Cha penalty, which naturally took care of the Intimidate penalty. Ultimately, I guess it doesn't matter too much, and your +3 bonus to Intimidate gives the same net result. I guess it depends on which you'd rather see: half-orc wizards or half-orc sorcerers. Personally, I liked the idea of half-orc sorcerers better, so I went the route of an Int penalty.
Both - I included the +1 to skill points to both races because it's one of the two traits humans are most known well known for. I feel that an extra feat is something that should stay human only (I'm looking at you strong heart halflings) as that is their major strength as a race. The skill points while useful, aren't overwhelming powerful help flavor the two races as being half human.
I also gave this to my half-elves, but I never considered it for half-orcs. Nice.