Personally the only reason I use the registrations is because I do my nut in looking at the numbers. Otherwise, the number system is a better way of doing things, I just can't stand the numbers.
That being said I really want to be able to assign different registrations to different aircraft models. Like Boeing 707-320B's have different registrations to 320, 420, 320B Adv etc. I would find that most useful for looking at large schedules and working out which aircraft is what type. I've been looking and adjusting my B707 schedules and I would like to look at all my B707's in the scheduling page so I can move routes around. If I had different registrations for a different sub type it would make it a lot easier identifying the model each aircraft is, because then I wouldn't end up assigning a long route to a -420 that can fly it but with virtually no one on board. But I can easily identify the aircraft to move a route that it's better for a -420 to fly as opposed to a -320B. It was a problem I felt even more operating a 250 plus Fairchild Metro fleet spanning each type, you can't assign a 1000nm route to an earlier type and identifying them was a pain.
Defaulting so that you can sort aircraft most recently delivered, or defaulting to show unscheduled at top of the scheduling page, or even low utilisation (say under 6 hours) at the top of page would be very useful. At the moment if you create routes and then click assign to route it will take you to the first page of that aircraft and not the last, which is annoying. This problem is exacerbated by fleet replacements when you changing aircraft in the same fleet group. Meaning aircraft have been assigned a Registration that is somewhere in the middle of all your fleet not at the end.
It would be nice if the system only assigned a registration once, that way even if you remove a aircraft with a particular registration, that registration is never reused automatically by the system. I imagine that is a relatively simple thing to do. It would have also made changing a Metro I fleet to a IIIA fleet or such so much easier.
schro has the point that it needs a bit of updating in the usability stakes to make it workable for larger fleets. Although I find not being able to assign different auto registrations to different sub fleets annoying for any size, particularly when using aircraft with big differences in range between types. B707 and Fairchild Metro being two examples. I think there are a few usability tune ups to be discussed and implemented just to make managing things a bit easier.