Most of this is valid and well raised as issue, and most of it endures still in the current patch.
Most spells now present an upcast window similar to the Hex interface, but as you point out, and as I point out in my own spells-focused thread, that's not a workable solution in the long run.
You can pop out your inventory panel to sit open while your screen sis showing the game world, and you can use that to drag items to an open container, but it's not ideal and is very clunky. worse, putting things into and taking things out of containers is very labour intensive anyway - items dragged into a container with many things do not simply displace and add - you are forced to find an empty space to put them in, or else they swap with whatever you land on. Similarly, the window scrolls back to the top each time you take an item out of a container, and this can make retrieving several things from far down the list painfully annoying. these issues all still persist as well.
The 'wares' thing is a legacy form Divinity. In theory, you list things as 'wares', meaning that you intend to junk-sell it, and then later on, you can tell the game to 'sell all wares', which puts all wares-marked objects on the counter... However, it wasn't hugely reliable, and because you had to manually wares-mark each item, it didn't actually save you nay effort of clicking at all, at the end of the day. It was a pretty useless system then, and it doesn't do anything at all now, because it hasn't been fully implemented.
Beyond that, adding my second to the issues raised here.
