Eric Musco just informed us that Game Update 4.1 will increase the stack limit of items from 99 to 9999. Good call if you ask me!
Crafting Changes in 4.1 | 02.01.2016, 02:27 PM
One of the issues we have seen brought up quite a bit in this thread is storage space. Although we aren’t adding new bays at this time, one change to help with storage is that any item which previously stacked to 99, will now stack to 9,999. This change is coming in Game Update 4.1