Would be good if the pattern matrix let you distinguish different patterns by assigning them colors or pattern numbers.
Some sort of “scrap” pattern feature so you can keep copies of patterns you aren’t using immediately in the song, similar to buzz tracker’s patterns which stores numbered patterns for each track.
Also it might help to be able to see the notes and maybe track effects in the automation window.
By rightclicking, you can assign custom colors to individual slots, thus also to a row of slots (pattern).
Retaining pattern number is possible too - by default, Renoise is keeping things sorted for you but you can disable this feature - check out our wiki
As for the scrap feature, this is something I have thought about too. Not only because it’s a neat additional feature but because it would make it less likely that you accidentally delete a source for aliased slots.
Check out that discussion here