I haven't delved much into his life and it will be awhile with my pile of books on Grant to get through first - but I just found out that he was the highest or second highest officer in the old army BUT when he joined in with the Confederacy, he was only the 4th highest. From the little I read, he was pretty nettled about this and things went downhill from there with Davis.
So.... do you think, if he could have known in advance what his ranking would be and how Davis would be, would he have gone with the Union or the Confederacy?
Joseph Eggleston Johnston was the first West Point graduate to reach a Full Generals rank when he was appointed Quartermaster General of the US Army in 1860. No other General left the US Army for the Confederacy and, as such, he was the highest ranking officer to leave the Union. The second highest ranking was Samuel Cooper who had served as Adjutant General since 1852 but held the full rank of Colonel.
When it came to the ranking the Full Generals of Confederacy this was not reflected as Joe Johnston fell from 1st to 4th, with Cooper, Sidney Johnston and Lee all being bumped ahead of him. The reason for this was that Johnston had transfered from a Staff position as Quartermaster General (US) to a Line position as a General in the field and the rules for the Confederate army forbade Staff officers from using their seniority to take command of troops in the field. Confederate regulations also discounted brevet promotions when it concerned seniority, and as Joe Johnston's last full rank as a Line officer in the US Army had been a Lieutenant Colonel it accounted quite legally for his fall behind the three full Colonels Cooper (Staff), Sidney Johnston (Line) and Lee (Line).
Johnston was upset about this because nobody had bothered to inform him about how the rankings and seniority would be decided. Without an explanation he took it to be a public rebuke and a display of discontent by the Confederate Government of his conduct to that point. He may well have been jumping to conclusion, but Davis's letter to him dismissing his protests outright yet offering no reason for the change in ranking position did nothing to address his concerns, sooth his injured pride or convince him that he had the Government's confidence.
It is my belief that had he know ahead of time that he would have suffered a drop in seniority then, even if he did not know the reason why, he would still have joined the Confederacy. As his wife Lydia said to Winfield Scott when the US General-in-Chief tried to recruit her in his attempts to convince him to remain with the Union:
"My husband cannot stay in an army which is about to invade his native country"
Much like his friend and West Point classmate Robert E. Lee, Joseph E. Johnston first and foremost thought of himself as Virginian, and where Virginia went he saw himself duty bound to follow.