You are comparing apples and bananas.

Lee was a theater/army commander who had to command an entire theater of war which included a great deal of military administration as well as numeroud reorganization of his army due to casualties int he senior leadership.

Forrest was a cavalry commander who commanded at brigade, divisioan and corps. He operated independently on occasion or at the direction of an army commander. Nowhere near the responsibilities of Lee.

I'll respond on that 9 month period in a sepaarate posting

1) James Longstreet--Never lost a defensive position throughout the war and fought in virtually every major battle in the East.  He also understood before any of his peers how changes in technology required changes in tactics.  His new tactics were a virtual blueprint for the trench warfare of WWI (50 years early).  Eclipsed by more aggressive generals like Lee and Jackson, he came to forefront late in the war.  His defense of Richmond was so good that Grant almost lost his job over the heavy casualties.

 

2) Albert S. Johnston--Considered the best Southern general prior to the war, he was also the highest ranking Southern General.  Although he only fought in one battle (Shiloh) before he was killed, his performance there spoke volumes.  Prior to his death, Confederate troops surprised Northern troops and nearly routed them.  These were not your typical Union political appointees and raw recruits.  Among the retreating Union generals were both Grant and Sherman.  Their troops had been battle-tested at Fort Donaldson.  After Johnston's death, his second in command, P.G.T. Beauregard halted the Southern pursuit of the fleeing Northern troops, allowing them to reinforce and reorganize overnight. The Union reversed the outcome of the battle on the following day.

 

3) Joseph E. Johnston--Often not appreciated because of his Fabian approach to battle.  He was known for avoiding battle before superior Union forces (as he did during the Peninsular & Atlanta Campaigns).  When he did choose to fight, he proved capable.  He fought McClellan to a draw in the Battle of Seven Pines, at a substantially lower cost to his army than Lee, who took over when Johnston was wounded.  He defeated Sherman at the Battle of Kennesaw Mountain, although outnumbered 2-1.  He was the highest ranking officer to join the Confederacy.

 

4) Nathan B Forrest--His use of mobility and guerilla tactics are still studied today.  His ties to the KKK have soured many on his reputation, but his battlefield methods were effective.

 

5) Thomas "Stonewall" Jackson--his use of mobility to defeat a divided enemy force during the Valley Campaign is still studied today.  Although widely considered the best Confederate General, I've rated him lower because of his over-agressive attacks often were counter-productive and resulted in heavy casualties to his own troops.  While their is something to be said for an aggressive attack, his victories could be pyrrhic (Mechanicsville & Malvern Hill).

 

I have not included Robert E Lee on this list for a reason.  While his leadership was clearly without peer, his generalship was (like Jackson's) dated, overly aggressive, and often pyrrhic (Gettysberg, Seven Days).

I believe that Joe Johnson's greatest liability was that President Davis seemed to have no use for him.

Joe Johnston's greatest liability was that he would not fight. A Southern general who did not fight before Richmond would have let McClellan start a formal seige - and McC would have won. He did magnificently maneuver himself out of Atlanta in time for the 64 election.

Longstreet was magnificent apart from his defensive abilities he was the guy that launched the attacks that smashed two union armies (2nd Bull Run and Chickamauga) and damn near a third - ?Spotsylvania (first of the Wilderness battles)

AS Johnson. I have never been sure about. Everyone thought he was good, and he had a bad hand to play in the west. Did not do it that well (but it was a very bad hand). First day at Shiloh was a mess and Grant and Sherman had things pretty much under control - see Bloody April for a minute by minute account. But most of the good civil war generals badly screwed up their first large command and he did not live show he had learned.

 

What about Dick Taylor - good division commander in the east and did a very good job in La/Miss later in the war.

 

Kirby Smith - his part in the invasion of Kentucky was well done and he was the 4/5th ranking Confederate Lt Gen.

 

The Geniuses of war often go unrecognized (probably because of the  natual distaste for the brutality that goes with war).

 

I must disagree with the notion that there were ONLY two in that war.  The truth is that you have to be smart to succeed in war, because the stupid tend to get weeded out in a hurry.