I feel like I've gotten accustomed to the layout of the raid store at this point - at least most of the character shards are at the bottom - that saves me a ton of scrolling. I think if maybe the swapped the location of the Raid2 items and the Raid 3 items (since Raid3 spends way faster than Raid2 in my experience) that might be the only update there that would provide significant benefit. I wouldn't want them to remove things from the shop though - as much as is in there already there's still times when I need something and have to wait several refreshes to see it come back around.
The change to the shard shop is annoying - I'm used to going to a specific part of the screen to find the items I'm looking for - and previously they were all on the same row making it even easier. Now the 360 cost items are spread across two rows, which is annoying, but I'm sure I'll adapt. Shards, GL tickets, and blueprints could definitely be sunk to the bottom though - I'm long past needing those shards or blueprints and there's maybe once a year at most that I'll even consider buying the GL tickets at this point. Why fill the top with things most players will never need again?
I'd really love for them to right-shift the events that I can't take part in though. Proving grounds, the fleet mastery items that I'm now locked out of, events that I've completed that can't be refreshed - moving all that stuff to the end of the line would reduce clutter there considerably.
I agree with most of your points though Seedy, and I second the idea that devs should try to think like their players. Really, I think that's ultimately a function of the QA team but maybe the QA team is overburdened as it is. All signs have pointed to that truth for years now. (yeah, yeah, I know... "hahaha you think they have QA," dear forumer, please don't respond with that...)