Everybody here made some good valid arguments.
The commander function is a great feature, which only should have been altered for BF3, not axed! Specifically remove the "enemy units spotted" audio and chat spam with just a blip on the mini-map. I cannot imagine attacking/defending Karkand for example - without a commander. I am solely referring to squad/team play when teams are even, skill wise.
The reason commanders are not so effective anymore - is because lots and lots of good BF2 players left the game 1 or 2 years ago. Hacking/Spoofing and BC2 drove the final nail. With the exodus of good players - team play was replaced by nade spamming/vehicle whoring, and a general selfish attitude - making commanding unappealing, to veterans and new players, alike. Why spend a whole round commanding, when no one follows your orders, defends the flags or kills the people flanking - for a lousy 20 or 30 points.
Even so - like Lex said, commanders are still largely responsible for the outcome of a game. 99% of the time you can still easily predict which side will win the game - just by comparing the ranks of the two opposing commanders.
Almost everybody I speak with, tells me the same thing: "I get bored of BC2 after 5 or 6 rounds, yet I can play BF2 the whole day." Like Soulzz said, the depth of strategy is what makes people want to play just "one more round", or play the same map (Karkand I/O only ) over and over again for years.
The omission of the commander is clearly a step in the wrong direction - I can only hope that BF3 will have other redeeming qualities.