@Xaiier
I must admit, I'm surprised the first two points weren't received as well as the latter two - those are where I feel at least basic changes are needed most urgently. I'm something of a pack rat; unless I'm sure I won't ever be needing a specific weapon, I keep it in storage. Seeing I'm new to the game and haven't thoroughly tried out most of the weapons yet, I sell weapons approximately... never. I just finished my first Nerexelin playthrough, and towards the late-game, the inventory situation got fairly horrendous. Without any way to sort items, I was forced to jury-rig a system: first row was ballistic smalls, then energy smalls, then missile smalls, repeating for each weapon size. When I wanted to change home bases, it took several minutes of clicking to transfer that inventory to my ships, and again when I got to my new base. When my collection of ballistic smalls outgrew it's one row of slots, I had to move 90% of my inventory down to give it a second row. Whenever I encountered a new weapon I had to manually move around the other items on its row to fit it in the proper place. (I generally sorted by damage type, then range within rows) By the end of the game, I had three 'pages' of items to sift through whenever I went into my inventory.
In other words, manually managing large numbers of items in the current system is a pain in the ass, both in terms of clicks needed and information density (I'm sure there's a more space-efficient way to display the items). I was only playing with the mods Starsector Plus, Interstellar Imperium, and Tiandong Heavy Industries - for my next campaign I want to add another ~6 factions - the sheer number of new items that'd introduce and the inadequacy of the current organizing scheme is the reason I'm considering only adding a couple more factions.
I realize this is only a major problem - for now - thanks to mods, and I don't expect the game to bend over backwards to cater to people's playstyles, but as I noted in the post I think a better organization system will be very necessary in the long run, unless the core game's weapon set is largely finished, which I was under the impression wasn't the case.
While I agree that scarcity and the search for better gear is an important gameplay element (thus, I play with Omnifactory off, and rare ships and expensive ships on), I disagree that optimizing the search constitutes not playing the game. It feels okay early game when you're building up your small fleet - and by design that's when you'd be unable to afford the fee - but late game it feels ridiculous pulling my battle fleet off the front line of an ongoing faction war to go around checking SpaceMarts. I end of trading my battle fleet for a few vastly speedier combat freighters that don't burn dozens of supplies a day - I don't see what gameplay that gives me that is superior to my proposed system.
I understand your objection to the first of the two 'possibly' suggestions - it's a time-saving measure, again, so that I don't have to pull my battle fleet out of an ongoing war to fetch replacement ships stashed in another system. Why do I have to jump in a frigate and fly over there to fetch those myself? I personally would prefer the ships are assumed to be traveling under a neutral flag and in a convoy large enough to deter pirates and would always arrive safely, but I left it open-ended, as I'd be happy to see this system in any form.
@Tartiflette
I grant you, I went a bit overkill specifying filters - sorting by damage type, for example, I probably wouldn't use much, nor grabbing items based on slot size/slot type/damage type. What I really do need, though, is a better way to keep the good stuff in one area - and sorted by things like slot size and type - while keeping the chaff off the to the side without selling it entirely. I didn't put it in my original post, but I describe how I've been managing my inventory so far in the first half of this one, and it is a pain. Even giving me a few different folders/boxes/sub-inventories I could sort items between would be immensely helpful, so I could have one for items I'm actively collecting for refits, one for good items I don't have an immediate use for, and one for items I don't care for as much but want to keep around. With that, the current sort-by-size would probably be good enough.
Tags are the most pipe-dream of my list of hopes for the inventory system; I'd like some way to separate the high-value items I'm earmarking for retrofits and a way to easily spot weapons I'm after in markets (Sabot Pods look a lot like other missile pods...); a right-click option like "tag all of this item -> select color -> orange' type system is what first came to mind, but I'm in favor of any system that lets me do those two things.
EDIT: A+ on the suggestions in the UI and Interactions Streamlining thread, btw. Thanks for the links, I'll be reading through them as I have time