A list of (most) things about the game that are not properly explained to the player:

✓ XP gain on level selection screen: not specified that it only affects profile XP

✓ Profile XP: never mentioned that it's only gained in Normal mode

✓ Custom maps: it's not clarified that excess resources mined are not given to the player after game ends

✓ Towers: holding upgrade or ability button applies this action to every tower of the same type - never mentioned
Note: mentioned this in general hints and added a "holdable button" mark

✓ Detailed mode: mentioned only once in one of the tutorial levels, which people often don't pay much attention to
Note: tooltip will show up near the button if player never used it (tutorial levels do not count) and is playing for at least 3 minutes. Also mentioned once again in general hints

✓ Modifiers: players are often unaware of their existence even after unlocking them and often don't understand how to use them
Note: added some general hints about different modifier types. Tooltip will show up when player encounters the Modifiers tab for the first time

✓ Inventory: "hold to select" not mentioned
Note: added hints to the inventory's item info pane if no item is selected / inventory just op

✓ Custom maps: "drawing" mode for placing / removing tiles is only mentioned in old patch notesened
Note: added more detailed descriptions to the info overlay (big info button)

✓ Trophies: it's not made clear that effects like "-0.5% towers upgrade price" (Cannon trophy) apply to all towers, not just the one the player got a trophy of

% Missile: LRM is not explained
Note: added global hint for the LRM mechanic

✓ Inventory: no mention of the "open 5 / 25 at once" functionality for chests and packs (now shows a "button can be held" hint icon)

✓ Stage 6: gems are not explained at all (Gem menu added in 1.9.0)

% Score: its sources are never explained (but can be viewed in the "live statistics" during the game)

TODO:

• Maps: tile coordinates are not named (what is this random "3:17" in top right corner?)
• Miner double speed: not explained anywhere in the game
• Inventory: 500 bases / portals cap is not mentioned

Can't find a way to easily explain this, may need some kind of a handbook feature:

• Star research: it being impossible to complete is not obvious
• Prestige: no proper introduction