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Not really a trick question.As we know... if you put in ½ cup vs a full cup, the smaller cup (½) will boil faster than the full cup.If you put in a full cup, vs two half cups, one would have the same amount of liquid, just different containers, so one would expect them to all take the same amount of time to boil.Likewise, if one put in ¼ cup, and 3/4 cup, one still has 1 cup of water, and thus everything boils about the same.There will be slight differences, which I would attribute to the uneven distribution of microwaves inside the microwave, as well as the ability of the container to act as a heat sink.

Yes there will be an effect where you can get a single full cup at the centre of the microwave, where the microwaves are normally more intense, where as the 2 cups will be circling around it

I got 2 identical polyester beakers with capacity 400 mL to the brim. I put 100 mL of water in cup A and 200 mL of water in cup B. I placed them in my (rotating base) household microwave, centred on a diameter and equidistant from the centre, and started irradiation at full power. Cup A started to bubble at 2 min 10 sec, cup B not until 2 min 45 sec.

I got 2 identical polyester beakers with capacity 400 mL to the brim. I put 100 mL of water in cup A and 200 mL of water in cup B. I placed them in my (rotating base) household microwave, centred on a diameter and equidistant from the centre, and started irradiation at full power. Cup A started to bubble at 2 min 10 sec, cup B not until 2 min 45 sec.There may be all sorts of electromagnetic and geometrical considerations involved, but the answer to Will's original question appears to be "the smaller cup, by about 20% if it contains half the volume of the other".