Our timetabler went on a couple of courses, and then produced this years timetable flawlessly, using Nova T. There's no reason on earth why it'd be a huge issue to retrain people. The overall functionality is the same across all MIS's - if it wasn't, they wouldn't be MIS's. The difference is where things are and workflows. Look at the switch from Office 2003 to 2007/2010 - most people make the transition easily.
I highlight ease of use etc, because I seem to remember elsewhere in another thread someone (not pointing fingers because I cannot remember who) saying that training staff is well down the list of priorities with a new system. Not to bring that argument back up here again, but if you are going to change a system because, as seems to be implied here, it can be developed by this that and the other (none of which I am particularly against!), at the expense of a difficult to use system by the people that use it most... then I'm sorry but to quote above 'they're not doing it properly and it should be questioned'. I mean just how long has it taken your key staff to learn a system enough to be confident and proficient in their job? your timetabler for example?