The major complaint, that I could see, was that Puri's were only buy able 1 at a time.
Purified Fusion Stones don't stack, for good reason. The way the Arcane Transmutor works is that you can't stack any item in there unless it transmutes EXACTLY into something else with no remainder.
Example: You put 5 Tier III runes in the Transmutor and you get 1 Tier IV Rune. But if you put 6 Tier IV runes in the transmutor, you don't get 1 Tier V and 1 Tier IV as a remainder, do you?
So, for Purified Fusion Stones to stack you'd still have to break the stack apart to use them in the Arcane Transmutor. Bad system (I'd certainly not want to do that every single time).
So, this solves the issue of "Purified Fusion Stones can only be bought 1 at a time QQ". Well, now, you can buy them in increments of 5/10/20 up to 50 times each, and they stack over 50, for the same price as buying just a single purified fusion stone.
This is a solution that is 1) Fast. It doesn't require Runewaker to introduce a patch to the game. As it stands now the Gift boxes are only stackable to 10 or 20 (depending on which one you get), requiring a patch to implement, then more item shop testing to do. 2) Accomplishes the main problem at hand; Purified Fusion Stones can now be bought in compact form, more than 1 at a time. and 3) Has the least chance of messing anything else up.
I for one love the new system. I can now stack 1000 Purified fusion stones in a SINGLE ITEM SLOT!
If PFS's were to stack, they'd probably only stack to 99. Meaning I would need to take up 11 item slots to store 1000, and to use one, I'd have to Shift Right click to break the stack down to 1 each every single time. Again, no thanks.
This is the best solution for Purified Fusion Stones that doesn't cause the most headaches, both from the backend and the front.