Exactly Youngjin, I believe I was the first mention (arrogant strut) the problem of TJ being a medic and having the rank of an officer back in the days of SGUS. If she was say, a corporal or sargent that would be acceptable (most of the time with rank comes higher skill set, though not always I've seen some privates CMT class 1). If she was an Lt, she would still be in medical school not on some off world base. To be honest its not hard just establishing characters rank and roles, a simple wiki search would of removed any queries or questions that rattled around in their minds, however they must still be in the mind set up 'only main characters can be officers'. Greer being the exception to this rule but he was relegated to 'man with gun' rather than 'advisor/lead for on world operations and fleet defense' since USMC do that strange thing called fleet protection. In a situation like SGU it should of been more about experience than rank itself, what if for example the highest ranking person there was a clerk Mjr and there was a SFOD Sargent, who would you honestly trust for doing operations?
Back on SGA, again I agree (my opinion starts here) it should of been a three tier operations, scientists, military and then the IOA. Each one having a lead, IOA lays the ground rules and the other two follow and are there to advise to the best of their ability but the decision for 'green lighting' operations remains with the IOA lead. A Colonel would never go out on the ground unless it is for 'face time' or to survey an area, usually the ground pounders are Majors and below.
So here is my obvious hindsight suggestion. In SG1 it was understandable why the groups had many officers of higher ranks, because of say experience needed for the unknown (using what was available). As time grew on, the SGC became an independent military force initially combining from US Forces (Navy, Army, USMC and USAF) and into a multi national EDF (Earth Defense Force). Anyone who joins this new structure has their previous rank removed and has to start again, this is similar to how special forces work, when you pass and are entered into the regiment (using British Forces here as an example) you go back straight to trooper/pvt (for nco) or Lt (for officers) because those who have newly entered don't have the experience for commanding this kind of people or the operations they do. For those wondering about pay issue, think about like this; Do you want the people out there fighting a hidden war to be concerned about pay? Or do you want the explorers, the people who jump at the chance of something frighteningly new, people who love their job. That is just me really