I agree with most of what you are saying.
IMO, TD% for a QB is the #1 stat to measure a QB by. Scoring TDs is the primary goal of the offense, above yardage, TOP, turnovers, or anything else.
You win games by scoring more points than your opponent, period! Not to say that those other things do not factor into the equation, but if TD% is not the top of the list then the list is flawed because that is the point of playing the game.
Aikman is an anomaly in that he was a great QB who threw relatively few TDs. 15 of the top-29 QBs with the highest TD% are in the HoF. 3 of those top-29 are still playing and therefore not eligible (Romo, Peyton Manning, & Philip Rivers) so that is 15 out of 26 eligible are in. That tells me that TD% is a very telling stat for a QB.
A turnover, while a seriously negative play, does not always lead to points, a TD pass ALWAYS results in at least 6 points, without fail.
Obviously TD% is not the ONLY measure of a QB but it is the primary one INO. After that I would go with Yards per attempt, then turnovers, then Completion %, then wins, then sacks. I have my own rating system that takes a lot of factors into account but TD% has the highest weight in it.
You can throw more INTs, complete fewer passes, gain less yardage, and get sacked more often and STILL win the game. You cannot score fewer points and win, it's that simple.
In Aikman's case, we had a dominant running game and a RB who was money to score inside the 5 yard line. Emmitt is the all-time leader in rushing TDs for a reason. So Troy didn't need to throw a lot of TDs for us to win games, but he got us into scoring position a lot. The same can't be said of most QBs though so using Troy as an example is kind of stretching the point.