From a mathematics standpoint you really can't call Dinosaur underperforming because it was a fully utilized attraction; they weren't sending out empty vehicles (which does happen on other Disney attractions, like Little Mermaid).
That has nothing to do with the ride quality -- I think Indiana Jones will be a better attraction than Dinosaur was -- but from a parks operations perspective the switch isn't going to change much for Animal Kingdom. Tropical Americas as a whole will, though.
Well, I believe Disney looks at more than just does a ride send out empty vehicles.
They are interested, particularly nowadays, in lightning lane sales, which have a very strong correlation to demand (which is correlated to waiting times). Dinosaur's lightning lane sales were a tiny fraction of FOP, Guardians, Rise, Tower, etc.
Disney surely considers the appeal/ demand of the ride in terms of whether it has an impact on guests desire to return. Part of the ROI analysis of these rides is whether they help create an impression and a desire of "I want to go back and ride that again..." Consider the impact and effect of FOP on most guests vs. Dinosaur.
Finally, I don't think Disney wants super long lines (despite the cynical take that they do to increase LL sales), but some lines are effective because they help spread crowds out, especially in a park with few rides, like Animal Kingdom. The decreased demand of Dinosaur correlates to greater lines at FOP, Kiliminjaro, etc.