What's been most apparent to me so far is the lack of visible information. I assume most of these things are planned but I am still happy to provide feedback.
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No star information re: habitable planets, colonized planets, etc. If this is a conscious choice, I'd counter by saying that it is important to restore this information. We know now what types of stars are most likely to be habitable. I'd suggest adding something similar to what Endless Space does where it tells you before you visit a star the odds that an adjacent system can be colonized and what you might find there.
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No details page for ships (I know this will be added), but it is particularly important for colony ships. I would suggest having this information visible without needing to go into a further page.
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No summary screens at the beginning of the turn, so on a larger map I might end up struggling to see what has been completed from turn to turn.
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The research page's interface is claustrophobic and confusing. Perhaps a return to GC II's method for this.
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I have to hover over ships for information about what they do in the build list, but when I click them I still get a picture. That image should have ship details (I imagine it will).
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The game seems to be trying to automatically place my improvements but when it places structures in translucent tiles, I keep thinking I double-clicked a building and am queuing more than I intended.
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The game doesn't give rush-purchase confirmation or options.
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Everything should be right-clickable for more context-dependent menus and information screens!
Some other brief thoughts: that ding ding noise at the beginning of a turn...not so great and made me mute the game, which is frustrating since hopefully part of the alpha is testing the sound systems.
I'm seeing the 2x, 3x, 7x tile improvements like we saw in GC II, but the icons don't seem to mean what I think they do. It might be worthwhile to develop new icons and ensure more clarity.
I have unlocked benevolence and malevolence at the same time. This should not be possible. How Ideology works is currently not clear at all.