I'd love to see something like this, as well. Currently, logging into any site where I have multiple credentials saved in LastPass is a frustrating experience, as the options appear in what seems to be a random order, and that order occasionally changes (especially noticeable with Google, where I'm up to 6 stored credentials now).
Being able to manually sort the autofill entries would be great. The new popup appearance in the latest version of the extension (4.1.39 in Chrome) already looks like it should allow drag-and-drop reordering, with the "paper cards" appearance, but it doesn't.
At the very least, sorting the entries consistently -- ideally, alphabetically by username -- would at least make finding the desired option in the list less painful.
Being able to hide certain credentials in the autofill popup would also be useful, though if you only have time to make one change, I'd vote for sorting.