There are several options for accessing specific overlays that could be implemented, one of which should probably be keyboard shortcuts, regardless of whatever other methods there are for accessing these information overlays.
An unobtrusive tab on the left side of the screen, much like the one on the top which contains resource information and other buttons could be used to select specific modes/overlays. There is no need for this tab to always be present; there could be a button beneath the turn button which expands this tab. The buttons for the overlays themselves would not require words on them; that would intrude into the screen too much. Instead, icons should be used for a more compact format, and tooltips should be used (regardless of whether icons or words are on the actual buttons) to clarify the function of the specific overlay in question.
Alternatively, there could be a second row of buttons on the tab at the top of the screen, specifically for information overlay buttons. I'd prefer having them on the left though, as having more things on top might intrude upon the system sidepanel (and as Geoff points out, that space might be used for additional resource information in the future)...
As for adjusting the stealth threshold, this could be a more general issue for when a player wants to specify any specific aspect of an information overlay. Presumably, there need be only one information overlay active at once, so there shouldn't be a problem with a small pop-up window requesting specifications for the overlay - what the stealth threshold should be, for example, or which specific planet environment to flag. The pop-up window would disappear when the overlay is deactivated, and reappear where the player left it when it is reactivated. This way, it can be put in a prominent location when the player first activates it, so he'll notice it, but can be tucked away in a corner once he knows its there and what its for.
Another possibility would be to have these options be preset in a different options menu (not ideal) or to have the options be always visible next to the button that activates the overlay. The latter option has the advantage that every option for which the player can set a specification is made quite obvious, but the disadvantages are that it would further intrude into the galaxy map, and if the tab is collapsable, players who use keyboard shortcuts to activate the overlays will have to use the tab to set specifications anyway, defeating the purpose of keyboard shortcuts.
On a side note, in addition to specific information overlays, the player should have the option of viewing the galaxy map from the point of view of a different empire (using only known info about that empire, of course). This would mean that in any specific overlays or other UI elements, the selected empire's info would take priority over all others in the case where not all overlapping info can be shown. This would be particularly useful when determining if a specific ship or fleet can be detected by a certain empire, for example (the other empire's known detection levels may even be taken into account, so any objects belonging to the player that the selected empire can't see would be invisible to the player himself with this option). It could perhaps be controlled from the same panel as the other overlays, but there would have to be a distinction between it and the other options to imply that it can be operative at the same time as any other overlay.
Geoff the Medio wrote:We also probably want an empire fleets list somewhere, which I had pondered putting on the left side of the map screen, although such a list could be just part of a separate sortable list of all objects on a separate screen or floating window...
My opinion is that there should be several separate windows for colonies, fleet lists, known planets, etc., the buttons for which could be arranged on the bottom of the screen like in MoO2, which I thought dealt with those things very well. (There would/probably should be a bit of redundancy between these screens and the information overlays.)