I find you're unfair with GalCiv 3 ,even if it's "so that we can make sure GalCiv IV is better", in comparaison with GC 2.
I don't know on wich version of GC3 you played for your example, but it's certainly not the 4.1 because main part of your critics are false.
I've never played GC2 so I can give you my first impression based on your screenshots.
GC2 _ "the UI is pretty clean" with two-thirds of buttons and information' cells hiding map with empty space, with an buttom bar almost empty with several obscur icons with exception for the graph and the tech buttons. All first information are packed on the buttom where it's more unconfortable to maintain your look and where it's the last screen's area where I'll have a look because I grew up in Europe where we learn to read from top left to buttom right. I guess it's the same in US.
GC3 _ "No on-screen direction on what I should do". The first thing I see starting a new game is my planet selected with my hovering cursor instantly opening a pop-up window with "queue empty" as a boundary between two sorts of information' layout. Exploring further the first view, I find a top-left rectangle with "not researching". Maybe there is something to do there. To be sure, there's a reminder "research" on the buttom right preventing you to pass your turn before selecting a tech to research.
GC3 _ "No on-screen explanation on what the ships do". Just maybe their names: colony ship, constructor, survey ship, scout. Do we really need more to understand what's the purpose of these ships?
GC3 _ "No anomalies (...) for my survey ship (...) so I just move it". Because "automate" is more visible or obvious than "command" button to give order to your ship to act by it self? We could replace them by a "be yourself" button or "live your own life" (a little bit too long).
GC3 _ "No hint on that it affects things in range". So you click on a constructor and discover an hex centred around (what you don't have with any other ship) but you don't understand that there'll be an effects area inside these edges? I'm not Sherlock Holmes, but I directly understood that first time I used a constructor in GC3. For sure I'm not alone.
Here are first points of turn 1. I won't go further because I should pass my day on it and also this topic is not a debate between GC2 and 3.
Then I'll answer to your question about setup screen to improve my personal pacing preferences as player:
1. Don't add unwelcome pop-up advices or flickering edges coming on every 10 sec or followed by 5 others in a row disturbing me from my game. Many games now take players for dummies stopping game or polluting screen to "explain" how to play. Let me play in peace, please, and discover the game by myself. It doesn't mean "do not give any information" but "give me information when I ask for it with a direct access to it" what I already encounter pretty well in GC3 with pop-up when I stay with my cursor over something I want to know more about.
2. Continue to use transparency to let me see what stay in background and don't have a hard break between current map and information windows.
3. Simplify minimap. I can only make out influence areas and star points. Ships, planets, anomalies, rally points (these ones, I can also see other players' ones what is unfair and useless, polluting my minimap) are undistinguishable without having to zoom in a lot. For that, I'd better do to watch directly on main map. I use minimap to have an overwiew and easly pan the camera on great distance. For boths aspects, I need to quickly and easily be able to discern wanted locations.
Edited 30/07: Replace minimap by a large strategic map called/closed by pressing a key as we can find in fps games on which we could easily spot information and plot markers.
4. A suggestion about starbase: when you select a module to construct (before to start construction) maybe it could be interesting to have affected things colorised with an overlay so you could directly see if there is an benefit to choose this one. Same idea with constructor travelling through hexs with potential affected things colorised.
5. About color, colorising text and use pictos to easily identify possibilities with idiologic dilemma could be a nice step back to GC2, but with the new idiology system (what is a feature I really hope lots of improvement in game fun and deep relations between civs) and 14 different idiologies it could be hard in practice to memorise refered color and picto for each idiology.
6. An enhanced mix of GC2 and GC3 building list. In GC2, buildings have a second string explaining what brings this last, reuse it but replacing text by the direct value of given bonus (e.g. +10% (approval picto)). In GC3, there are filters to sort buildings by types but they keep all buildings in the list. Set these filters as real filters removing all non relevant buildings so selecting research filter only show buildings improving research basically sorted by biggest bonus value on top with possibility to sort them by turns cost to complete.
So we'd had on left building's icon | in centre two strings with name above and given bonus beneath | a number followed by a hourglass on right.
I don't know how many icons there're with the new drag and drop system to build but if there're a lot I fear it becomes a mess of multiple icons.
7. Give possibility to minimize "summarize", "planets", "fleets"... windows and minimap and hold them minimized until I request them.
8. Use filters or pop-up icons to avoid to have to scroll through 30 listed things or to have to open 1, 2 or more windows before to get what I want. E.g., in GC3, if I discovered 40 planets colonised by me or available to colonisation, I have to scroll a lot to find information about one specific. Also in GC3, if I want to open United Planets window, I have to open Diplomatic one first then seek the button to open U.P. window. In GC4, I could hover the cursor on diplomatic icon what open above it icons to open U.P. or Treaties. Also we could use flags to determinate role of fleets or planets. In GC3, to more easily find back a specific planet I have to rename them based on their role (Food 1, Money 1, Tech 1, etc.). In place, we could have to just attribute a flag (the best would be to allow player to customise them) used in a filters' system.
9. In GC3, population max cap is determinated by planet's class, it would be nice to see this piece of information directly shown in-game hovering planet class value for example.
About game tempo now:
1. As a GC3 player, I find early and mid game have already a good tempo because it's a run to achieve most interesting galactic wonders before AI, a run to find ressources (antimatter for Hyperspace Project, Artocarpus, Arnor, Monsatium, Techapod...), a run to find best planets with high class value. Even if you don't meet other civs, you're form start engaged in this run to set up a more favourable position. In my games, tempo slows down in late game when AI persist to build 7 hexs move speed ships and take 20 turns to build a big ship when I build a full fleet in 4 turns with ships able to cross 165 hexs a turn. Even giving all best techs to my ennemies and waiting tens of turns to let them integrate these techs, it's what make me feel the game is running on dead slow in late game.
Edited 30/07: We could even speak about "non met yet"/ ship range pressure. Personally, I don't mind to meet béni-oui-oui civs in 5, 10, 20 or 100 turns, they're all birds for the cat. The stress comes with agressive civs that will declare war on you as soon as they can reach your planets with their ships
2. Another point is the number of planets to colonise, to conquer, the mountain of little useless fleets to crush and others painful tasks are so many things making me feel spending my turns to complete the same repetitive and boring action. I know that the new core world/ colonies system should solve a part of that, but not for me. I already use a similar system in my games. I colonise few very good planets (15 max) and let AI's colonise all the rest, granting me ressources and wealth via friendly deals, galactic market or peace deal. I fear to be obligated to spend my time in a boring wide colonisation with this core worlds system.
3. I have a request for GC4 and to maintain a longer threat from AI, add an option in new game setups to let computer choose a random number of opponents. This way, until far late game I would never be sure that an ennemy is not suddenly coming in my back.
4. Add rare and mighty galactic disasters that affects alsmost every players and reshuffles a stagnant situation, forcing to adapt and rebuild your bases (I know it could disgust some players to lose a lot without being able to prevent it)
I don't know for you but for me, the most funny phase of a game is the early game when everything waits to be done.
To summarise, as player, I'd like to have needed information easily, shortly (concise form) and quickly available when I request them, in addition with customised management allowing automatisation (learn to delegate) to prevent repetitive actions, all that to help me to stay focus on the developement of my civ through long term events and evolving relations with other civs.