Matrix items are great and they work really well however some customers still like to use the traditional catalogue view filter.
I would love to be able to make all as single items but also make a matrix item that consists of all these single items so the customer has the choice of which method to use to find the product they want.
The original version of our product had a bug whereby 'Reference SKUs' could be created. This led to a number of display errors, search difficulties and performance problems. When we rebuilt our front end - now known as Themed - we did not support the display of 'Reference SKUs' and removed the bug from the CMS which allowed their creation. Matrix products work best where the attributes tend to be size, colour or similar 'systematic' values. If products need to be displayed in multiple places then Simple Products grouped into sub departments works well - particularly using the list view as Mark mentions. We will not be implementing this idea.
Under the new themed template, customers can view by list view and it show all products individually within a category. It also shows stock availability so they can pick items that are in stock.