Per year is indeed interesting, but you will bump on many inconsistencies and one more thing that will need to be more "careful" about (sometimes the year is confused by things like when the crack came). Yes it is already important to have correct year, but if it becomes a folder separator, it becomes way more important.
The suggestion of "good/original" (like a no-intro part haha) vs "rest" is also good, but again, you will face way too much re-organization AND you will end up with a huge "rest" category. So I don't think it will help.
There is one thing you need to consider Duncan! You have to look at how a user will LOOK for a title.
Imagine let say that you want to check out Obliterator. Do you remember the year? You definitely remember the name though.
This is why letter is good.
Also because it is the most "objective" metadata of a game. We even call game collections (or movies etc.) "titles" some times, exactly for this reason.
(that said, indeed there are games with more than one official title, usually because of region issues)
Another classification that could help you split things up (but even I don't like it that say it)... is to separate multi-disk from single disk. Multi-disk are way less than single disk, but because they are erm... multiple, still make the list big. Single disk, are WAY more, but only a single entry (plus variances) per title.
The more I think of it, I believe letter is the most clean/straightforward/objective.
Note that I believe whatever is chosen, it has to become the splitting option for ALL machines (when splitting is needed) -i.e. for the whole TOSEC.
Hope you find a way soon.