If the game box isn't meant for storage, the entire world is doing it wrong. Board games have always been packed back into their boxes after use. LCGs shouldn't be any different, apart from the spilling over into other boxes a few expansions later - boxes which the expansions no longer provide. Go7, Basically Wooden and others provide decent solutions to make the most of boxes which weren't designed to hold the components neatly.
The LCG boxes are intrinsically terrible for tidy storage only because FFG cheap out (particularly after the merger). See Paizo's Pathfinder ACG for one of several proper ways to do it - the core has slots for every expansion box.
FFG's boxes have always been awful. Ok, bigger, and so able to store things, but terribly design for storing the actual game it comes with when unpacked. Doesn't matter if you are talking about the miniatures games, the board games or the card games. they are designed for 2 things in mind - holding the game until they get to you, and looking nice on the shelves of the shop. Yes, the new boxes are cheaper and flimsier, but they achieve exactly the same result and are much easier to dismantle for recycling. Note also that lots of games companies have bloody awful boxes for their games, that just leave loads of space for the components to rattle about in and get mixed up and possibly damaged once opened. This isn't unique to FFG.
Now, of course some people (including myself) use the substandard boxes (well... actually quite nice and sturdy, but bloody awful for practically storing the game they hold) for storing the expansions for the games... however, I don't think this is an unfair place for them to skimp on. If it stops them raising the prices, and reduces the number of boxes cluttering up my room I am all for it.
Note that the Pathfinder games are very different. They each have a limited number of expansions, and so they can design the box to fit the whole set from the get go. This game is not like that. It is intended for expansion into the indeterminate future. Do I like games that fit their boxes well? Yes? Do I expect every game to do this? No, it is usually an added luxury.