Some ways to merge vertices by distance (aka "remove doubles"), in edit mode:
1) Mesh > Clean Up > Merge by Distance
2) F3 operator search. Start typing "mer..." and hit Enter.
3) Ctrl-V to show vertex menu, then Merge Vertices > By Distance
4) The quickest: Alt-M + B (show vertex merge menu, B to select "By Distance")
I scratched my head a bit first too, but frankly "merge vertices by distance" is far more descriptive than "remove doubles".
The UI that pops up is just the operator parameters that used to appear when you hit F6 (eg try adding a Circle, see the parameters that pop up) It's better this is visible to users, rather than hidden behind some secret hotkey. As with previous Blender versions, operators are "applied" by default - you can change the parameters via the UI until you like the result. Once you switch operator, move on, or change mode, the UI will disappear and the operation becomes undoable.
To make objects visible/selectable/renderable etc... open the filter menu on the Outliner (top right, looks like a funnel). This lets you add more toggles to the items.
To move the view/selection/snap settings to the bottom just right click, Header > Flip to Bottom/Top.
Collections replace layers and groups (eg you can instance a Collection), though I haven't completely got my head round them yet. But they look quite powerful.