Consider this. Ability scores do alot of things that are not based on class or feats. Just looking at the raw functions (aka not class-based) things each score does, we see...
Str: + to melee hit, + to damage, carry capacity, climb/jump/swim checks, grapples/bonds.
Dex: + to hit ranged, + to Armor Class, Reflex Saves, Initiative checks Balance/Escape Artist/Hide/Move Silently/Open Lock/Ride/Sleight of Hand/Tumble/Use Rope checks.
Con: + to Hit Points, Fort Saves, Concentration checks, Holding your breath.
Int: Skill Points, Appraise/Craft/Disable Device/Forgery/Knowledge/Seach/Spellcraft checks.
Wis: Will Save, Heal/Listen/Profession/Sense Motive/Spot/Survival Checks.
Cha: Bluff/Disguise/Diplomacy/Handle Animal/Gather Info/Intimidate/Perform/Use Magic Device checks.
These are things all classes can and do use (every class uses skills, swings a weapon, makes a save, gets his AC hit, and takes hp damage) Now if you look at all the individual functions of the scores, you see that Strength does 5 things. Dex does 5, Con does 3, Int does 2, Wis does 2, Cha 1. (counting all skill checks as 1 thing if you want to make this more scientific, tally up what each individual skill bonus is worth).
If you were to see all the abilty scores modify and how many things a stat bump raises, you'd see the half-orc isn't so penalized.
Human/Half Elf: --
Elf: +5/-3 (net +2)
Dwarf +3/-1 (net +2)
Gnome +3/-5 (net -2)
Halfling +5/-5 (net 0)
Half-orc +5/-3 (net +2)
Barring class abilities, in things every character can/does do, dwarves, elves and half-orcs come out with an overall bonus of +2. Humans, half-elves and halflings all come out even, and poor gnomes get the shaft at a -2 net bonus (which is more than made up for in spell-like abilities).