This is a perfect example of how parts of the game have defianitely been upgraded, but still need more polish.
While I do agree in general that the game needs polish, I gotta disagree with you on the example here, Thayos. For SE to have automatically 'collapsed' our inventory stacks would've resulted in a lot of extra development. Not only that, it would be one-off development work, never to be used again.
For example, they'd have to iterate over every character's inventory, bazaar, and retainer inventory and bazaars. They'd have to then check whether or not the item is subject to extra stacking. They'd then have to figure out if there's an extra stack to consolidate. Etc. etc.
Not only that, but QA would be a nightmare. What happens if something goes wrong during execution? How do they ensure that your item count before and after was the same, for every item. Etc. Maintenance nightmare.
Instead, they made a very appropriate decision to use already-implemented in-game mechanics, and have users spend 30 seconds to 5 minutes to collapse their inventory, and not run the risk to experience any hiccup whatsoever. If SE were to 'polish' this behavior, they most likely would have spent extra weeks if not months tackling a problem which already has a workable, scalable solution, and diverting resources from other things.
It was a cost-benefit analysis where the cost far exceeded the benefit. The dev team clearly made the right choice here.