Well, they were different companies producing the sets and different people writing up the facts. Of course it's been so long since TMS season 3 has been released that there should have been plenty of time by now to make them for seasons 4 and 5.
The Simpsons had a fact track on one episode in the third season (and one of my least favorite episodes at that), and never did that again (though they do continue to put commentaries on each episode). A fact track was also done with Sesame Street: 40 Years of Sunny Days, I had hoped it'd be at the same rate as TMS season one but there are long gaps where there aren't any pop-up facts.
I remember when the first season came out, I was hoping Muppet Morsels would be a trend on all future Muppet DVDs (not just TMS). Then again, I can't think of many DVD releases that include a fact track (mainly just all that I've mentioned here).