I think prior 2005?, here in Europe most of early LED torches/flashlights, bicycle headlights, head lamps etc. were 4x AA/A powered. They've been made 3x AA/A since then.
This isn't very user or eco friendly as most batteries (alkaline or NiMH rechargeable) are being sold in packs by 2 or by 4. Also battery rechargers usually have 4 slots, not 3. Some rechargers charge batteries only by pairs.
The only reason for that I could understand is the compatibility with Li-ion batteries as 3x AA/A is voltage is quite close to 3.7V Li-ion voltage so only one board type can be made for both types of powering. Or is there something else behind the change?

It is a compatibility with the LED voltage. White LEDs have drop about 3V, whivh is close to the end-of-discharge voltage of 3 cells (standard Nickel-Zinc or alkaline and older NiCd rechargeable have technically 0.9V end of discharge rating, but with 1V they have given up about 95% of their capacity, NiMH have 1.1V).
The 4 nonrechargeable cell battery would add barely 5% extra runtime (allowing discharge down to 0.75V/cell), but needing 33% more cells, so more than 25% more wasteful.
The reason why early LED lanterns used 4 cells was first the "inertia" of using same 4 cells as with incandescents, but mainly the unavailability of the low cost low voltage drop constant current regulator devices (the special LED driver ICs like AMC7135 or so), so makers had to use either something more complex (so expensive) or the extra cell to get the extra voltage headroom to make the light usable with just a simple resistor (as that was cheaper to make, the cost of the extra batteries is not visible at the lantern sticker price).
When the dedicated ICs (cheap low drop current regulators) become available, the flaslight makers could get rid of the 4th cell without any cost penalty (or even save some money, as using those ICs is cheaper than the need to design the flashlight with larger compartment for an extra cell).

OK thanks, I see the reasons now. The option in using either 3xAAA pack or BRC 18650 in the same flashlight is just a nice side-effect of that change.

This annoys me as well. We have a 3 x D-cell Maglite, cells of this size are not cheap, especially when you want to use rechargeable ones. And as has been said, charging three is difficult, as chargers only work with either 2 or 4.

We also used to have a weather station that took three AA cells, again, what do you do with the 4th when it comes to rechargeables..?

There is a way (maybe not so straightforward ).

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repeat the cycle