For combat, you could perhaps get more damage mitigation from any type of armor, as well as a small increase to damage done with melee weapons (an extra 5% perhaps?)
For magic, there should be an increase in effectiveness of spells, their duration, or a decrease to magicka cost to help with earlier levels
For stealth, there should be simply a greater chance to remain undetected, or rather, if you chose a different specialization the sneak skill wouldn't be AS effective (like if you don't choose this sneak is only half as effective as it would normally be.
This is just a way to make people stick with specializations, for instance, you couldn't be the perfect warrior AND mage AND thief/assassin
EDIT: I've revised what I've said and changed them a bit down here
Combat: 5% extra damage with melee weapons, increased damage mitigation from armor, -25% effectiveness of sneak, destructive spells do 10% less damage (in addition to magic reduction from wearing plate armor)
Magic: Increased duration to DoT spells, spells more effective against people wearing a type of armor, -25% effectiveness of sneak, speed decreased significantly when using heavy armor
Stealth: Sneak is more effective, assassinations do twice as much damage as they would normally do, poison on weapons last for 3 strikes, destructive spells do 10% less damage, damage with large 2h weapons reduced by 10%