Just a couple of comments:
1) yes, Virginia, the other branches have ranks between line and flag. The mnemonic device for non-naval ranks is "Be My Little General" which leads to Brigadier General, Major General, Lieutenant General, and General.
2) during WWII, we had Admirals of the Fleet and Generals of the Army.
3) for some good information/discussion of the differences between Fleet Captains and Commodores, check out the ST:TOS core book.
4) as a prior enlisted man who is returning after receiving his college degree to fly, I must admit I have a unique perspective on the whole enlisted/warrant/officer debate. To become a warrant officer in the US Navy, one must first be a chief petty officer and apply for the position. If accepted, the chief is warranted/commissioned. The only real difference between a warrant officer and any other officer is that after a warrant makes chief warrant officer 1, he is guaranteed to be promoted to the rest of the chief warrant officer ranks. Another way for an enlisted man to get commissioned is to become a Limited Duty Officer (LDO). This is a lot like a warrant officer, except it may be applied for at the petty officer first class rank. Also, he actually has to get reviewed to be promoted. Both a warrant and LDO usually serve under a line officer and have senior enlisted personnel under them.
If you have any further questions, please ask.