I agree we need to choose replacements wisely. I intended to create a Jira issue to provide some guidelines, but now that this one is here I will use it.
ArrayLists are ideal for write-once-read-many situations. Linked lists are good for read/write scenarios. If you look carefully at Mini-language, you will see where I used ArrayLists in the model object fields - because the lists are written once and then read many times. I also used the trimToSize() method to keep them small.
Linked lists are good to use in the execution path - like in local variables.
Those are general guidelines, and there will be exceptions.