I don't really think there's such a thing as a "best commander" because each commander works best in different situations, although, having said that, there are some commanders that have some all around strong abilities that will give you an edge in most situations.

Some of these are: -Shock Rifles Frontline Tactics A very straightforward commander with very strong call in units and some simple but very helpful utility in the form of artillery and AT gun camouflage. The IS-2, Shock Troops and the KV-8 are some of the strongest units in their departments and, if that's not enough, you get the ability to camouflage your AT guns anywhere. Having access to some kind of artillery in the form of the Incendiary Barrage is also a pretty big deal, because it gives you a safe means to force your opponent's AT guns to relocate, flush entrenched positions, etc. -Guard Motor Coordination Tactics Another commander that gives you access to a bunch of good units and an effective ability. Heavy Mortars, Guards Infantry and T-34/85s. Mark vehicle is an extremely strong ability that will let your T-34/85s wreck a Tiger in a few seconds if you manage to surprise it and crew repair training is an useful ability that gives your T-34s a lot more freedom to roam around the map and punish your opponent's infantry. -Luftwaffe Ground Forces Doctrine All three default OKW doctrines are viable and strong but I feel this one in particular is more versatile and useful, even though some players only go for this doctrine for the MG34. Access to Fallschirmjäggers, MG34s and emplacements should be enough to make it one of the better ones. Valiant Assault is also really good, giving your infantry a definitive edge for a few seconds. Airborne Assault, on the other hand, is a bit more situational but a very strong ability nonetheless, if used right, will give your units an opportunity to assault your opponent while your Fallschirmjäggers wreak havoc behind enemy lines. -Airborne Company This is maybe the only commander you could say it may work in almost every possible situation. A very versatile commander, as it gives you tools to tackle infantry and armor alike, with access to many strong and flexible call in units and a what could possibly be the strongest ability there is. The P-47 rocket strafe run is an absurdly powerful ability. It eats enemy armor in a couple of volleys and if your opponent doesn't have some kind of anti-air it will pretty much completely deny your opponent's armor an entire area for a while. -Festung Armor Doctrine Panzer Tactician, Pak 43 and a Command Tank. A simple but effective commander. You also get access to hull down and railway artillery. While hull down is not terribly useful most of the time, in some situations can be of help. Railway artillery on the other hand is expensive and easy to evade but completely destroys static positions and any unit unlucky enough to get hit by one of the three gigantic shells. -Assault Support Doctrine Tiger tanks, strafing runs, opel blitz trucks, artillery field officers and fragmentation bombs. A nice commander with some synergies with its abilities. Your opel blitz trucks should give you enough resources to use your strafing runs to deal with infantry rushes and your fragmentation bombs will let you kill any AT gun threatening your Tiger. Officers are a nice bonus.

Those are the commanders I think stand out the most. I don't think my opinion is the absolute truth, though, and most commanders are actually viable depending of the situation you are facing. Also, I didn't mention the currently unavailable commanders like Advanced Warfare Tactics or Mobile Defense Doctrine.