I honestly don't think that Joomla! will ever ditch MooTools, but who knows. For sure not at this current state as they have pushed mootools 1.2 in Joomla! 1.6, which is going to be a very great update since MooTools 1.11, the one used on Joomla 1.5, is really old, limited and not maintained anymore for long time now.
You don't see it, but many times it happened I had to write custom MooTools core bits to have some of our RocketTheme's extensions work the way they work. I wish we all had mootools 1.2 in Joomla! but it will arrive, and you'll see the differences. In the other side I'm gratefully that Joomla! 1.5 is using MooTools, because enhanching core bits is one of the solid point of MooTools: Modularity.
Aaron Newton, one of the other buds at MooTools core team has written a good comparison between jQuery and MooTools, that reads suprisingly fair, I wouldn't link it if it wasn't:
jqueryvsmootools.com/
The way MooTools is, object-oriented programming, is what I think made Joomla! choose MooTools rather than another framework (please, don't make the mistake to consider all the js frameworks just javascript, they are all as good as different).
Thinking about all our RocketTheme extensions, I'm grateful we've MooTools, because updating, changing, fixing is much easier, just because of that little OOP detail. And this brings up another good solid point of MooTools: Maintainability.
The article I linked above, explains very well the differences. I, for the most, agree with all that is written in there. A big project, that predicts future updates, enhanchements and maintainable code will definetely fits perfectly with MooTools. I'm not saying that it is mandatory, I'm just telling you what was our main goal at MooTools.
And I feel surprised about the popularity argument. I really thought popularity was one of the very least subject to take in consideration. I don't choose a service or a product because of its popularity, but efficiency, quality. Sure popularity helps, that's though something that should come from the producer rather than the final user.
I have a very good example of a big project (
www.ape-project.org/
) that recently started. They've chosen MooTools. I asked them "why?" and they replied me:JQuery is a "browser framework" Mootools is a javascript framework.
I then told them that would of be great to read in a more detailed article all the reasons, and they are now writing it. As soon as I've a link I'll be glad post it in here.
Surely they will explain better than me, that am 100% involved, the reason they chosen one framework rather than another.