I have been working with template/skin design for almost 10 years now and while I am a bit spoiled working with forums such as Invision Power Board I consider myself having a fair understanding of what people want from a script and how to make things as easy as possible for the users so they will love the script even more.
As I understand it MT has just recently become a "Free" script and perhaps that is why the focus is on the output of the script and how you can redesign it rather than how to share your creations and using it to build a community sense, but in my experience the best way to encourage growth of a script, free or otherwise, is to make it easy to share designs and languages. This is something that MT is currently lacking and while I find the script easy to redesign and work with in terms of making it look the way I want it really need an import/export feature to make it easy for those that do not have the patience or skill to change the design on their own.
Language is another big issue, especially for the internal areas where clients/people from all over the world should be able to handle things in their own native tongue if they so choose. A feature that allow you to create, modify, delete and import/export language files is next on my list of goodies to be
Security is big these days and as a (very small) webhost I follow the security reports which now drop in almost on a daily basis and MT should be on the frontline to battle these spammers, hackers and other nasty bastards. In order to do that I would like a more evolved system for handling members and signups with options to filter out and deny registrations based on IP and/or emails. The possibility to tie the registration to a external registration service such as vox and OpenID is great, but I don't want to go through the hassle to finding the contacts for those services to report a potential troublemaker and would like to see a way to directly report the offender (unless this is done when you hit ban?) so they in turn can prevent him/her/it from re-register another account and continue spamming. Filtering out emails have been very successful for me in the past if it can be used with wildcards like *@mail.ru or just *.ru for example to get rid of those russian spambots.
One of the things I was looking for was the option when you make a new page to assign a template to it or the option to add a new one, but that seems to be a feature to be asked for. Having such a system would allow very quick insertion of different designs and if it can then be imported/exported with ease it could also be something people will spend time on making and sharing. For example you want to have different designs for your index, a category page and a specific page, then when you make a new page yoy can simply use a dropdown and pick the template you want to use for that particular design, or make a new one by typing in a template name for it. Maybe its just me who want stuff like this, but hey...might as well write it all down
Finally I really, really want to see a sorting feature for pages so you can sort the way they appear in the PageListing because its a pain in the ...you know where to not be able to filter the pages they you want them.
I have plenty more, but I have just scratched the surface and I think I should dig deeper before I open my mouth again to get a better understanding of the script