Mod Suggestion #1: Empty-My-Hand --- A lot of mods require clicking things with an empty hand, which often requires opening your inventory and juggling things around to free up a hotbar slot. How about a mod that temporarily "fades out" my current hotbar slot (mimicking an empty hand) for as long as I hold down a key? (As a failsafe, if some interaction actually requires that slot to be empty, you could either shift whatever's in the slot into the player's inventory, or just dump it on the ground.)
Mod Suggestion #2: Mouse Gestures --- With so many mods, hotkeys are in short supply. I'd love a mod that allowed binding a sequence of mouse gestures to an action---in a simple, granular way that wouldn't require a lot of precision. E.g.: To configure a gesture, Ctrl+Shift+MiddleMouse brings up a 5x5 grid of squares on the screen. You then move your mouse through the squares to define the gesture, and release MiddleMouse when you're finished. The gesture would then appear as a "hotkey" in the options (e.g. "Gesture1")---or, if that's not possible, perhaps the mod would then ask you to link the gesture to an allowable keyboard shortcut (likely one you wouldn't generally use because it's impractical, like NumpadMinus, or "+"). In-game, you'd start a gesture by holding down MiddleMouse, move through the same sequence of squares, release MiddleMouse, and bam: Hotkey fires.
Mod Suggestion #3: Precision Unloading & Locking --- Precision Unloading: Face an inventory, press a key, and any items in your inventory that match items in the target inventory are immediately transferred over. Locking: Hover over an item in your hotbar or inventory, press a key, and lock it in place, so that it cannot be moved until you unlock it. Taken together, these two functions would make it a lot easier to clear out a full inventory without having to manually sort everything into chests or worry about accidentally Trash Can'ing your pimped out TiCo Hammer---especially at the beginning of the game when you're doing a lot of manual mining and don't have an AE system or the equivalent.