3-man cons:
* you rely on 2 others for any 5-man content
* less impact on small BGs
* for anything outside of 5-man instances, you can't marshal the same coordinated power as 5+ boxers do
* may not be able to stack buffs as neatly as when controlling all 5 in your group (less effective skill/buff/debuff synergy)
* less versatile as you can't make sure you cover as many gaps (e.g.: resist coverage, CC types, etc.)

3-man pros:
* you rely on 2 others for any 5-man content
* less impact on small BGs
* only have to loot 3x
* less complex macro/skill setup

That's the easy stuff. I'm sure there are other details folks will add.