I started producing middle school shows before Junior versions. While attending an EdTA Junior Thespian Conference (somewhere around '96 I think.... before the acronym changed) MTI discussed their upcoming Junior line and had us read samples of what eventually became their first few scripts- Fiddler, Into the Woods, Guys and Dolls, Annie, and (I think) Bugsy Malone. We were given a sample or two to bring back to our schools, too. I gave them to my kids to read to get their feedback. Their response was, after having done full length productions, these would be a step down. They would rather try to shoot for a full performance and come up a bit short than be outstanding at a watered-down production- though, since they helped with the budgeting, they like the price range for the packages. (I still remember that conversation. At the time $500- which is what I believe the initial package was going to cost- and the added bonus of not having to find an accompanist seemed like it would be a boon from my end of things.)
The other issue I have seen is that when inundated with Junior shows, the kids don't always internalize that there is a difference between performing the junior and the full production: Once they perform Guys and Dolls, JR, they are done with that show and there is no need to do Guys and Dolls later on. This becomes even more pronounced among students when dealing with 'classic' shows as opposed to newer shows. Reading through recent posts here, it seems some of us have a difficult time bringing more traditional musicals to our audiences as opposed to Disney shows and knock-offs of Hollywood movies. When juniors are added to that equation it can become much harder to sell older actors on the canonical productions that give them a greater understanding of how musicals developed over time.