For me the major problems with the UI are as follows:
1) New features tend to get stuffed in wherever they'll fit. 3.3 did some cleanup of some of this, especially on the left and right panels, but also added a bunch more features. This even leads to some problems outside the strict UI - for example in a station which has a Black Market but not Contacts, you can't actually use the Black Market, because you need to go through Contacts to reach the Black Market.
Things like the station front page really could do with a complete rethink of the layout, for example, because a lot of new services have been added since the last big rewrite.
2) The design is set up to work with a basic HOTAS in VR, which puts a lot of limits on it - but I think there's two areas which could be improved on there:
a) More optional KB/M controls - being able to type numbers in with a keyboard rather than using +/- buttons
b) More "do the likely default thing" one-press buttons e.g. "unload/load all cargo" on the mission depots or the SRV transfer cargo page, "sell all" buttons in the market, default to "hand in all" on the search and rescue contact, etc.
3) Increasingly inconsistent design. The station interface is a good example of this.
- if you open the missions/passenger page, this replaces the station menu entirely, with the factions down the left and their missions on the centre and right.
- if you open the contacts page, the station menu stays on the left, and you get boxes to select for each contact, which then have a variety of UIs
- the shipyard page replaces the station menu entirely, but in a very different style to missions or commodities
or...
- if you open the commodity market, all goods in demand at the station are shown
- if you open the black market, only goods in your hold are shown
or...
- the material traders show materials in a grid, categorised by type and grade
- the material inventory on your right panel shows them alphabetically, filterable by grade but only the broadest type (e.g. you can't filter to "chemical manufactured") ... but it does show the capacity limits and how close you are, which the traders don't.
or elsewhere...
- the comms panels can be scrolled back quite a way to see older messages
- the info panel can't be: if you miss it, it's gone
4) Inconsistent display of data. For example:
- fractional combat rank is rounded down on the right panel, but rounded *up* on the SRV panel
- war progress is only properly shown on the right panel in the system, not on the system map, the local news articles, or in the journal
- which bits of UI-visible data are exported to the journal is variable
- a lot were fixed in 3.3 (friends list, for example, is now finally usable) but there are still some lists with an arbitrary and unchangeable sort order.
- in-flight data is categorised poorly: discovering a new asteroid belt is a top-priority centre-screen alert, while your power distributor failing due to lack of integrity is stuffed into a side panel
It's much better than it was in 1.0 in a lot of areas - you comment on the keybinding page, which is incredibly long and complex - but at least it now has categories and tells you where to find the new additions. And while I've been pretty critical of the station interface above, the 1.0 version would be completely broken nowadays. However, I think it's definitely the case that the game is adding new features faster than the UI team can properly integrate them.