Making one list from two lists by grouping them in a special way

You can use Join with level specification 2:

Join[list1, list2, 2]

{{{x1, x2}, {x3, x4}, {x9, x10}, {x11, x12}}, {{x5, x6}, {x7, x8}, {x13, x14}, {x15, x16}}}

MapThread[Join, {list1, list2}]

{{{x1, x2}, {x3, x4}, {x9, x10}, {x11, x12}}, {{x5, x6}, {x7, x8}, {x13, x14}, {x15, x16}}}

Flatten[{list1, list2}, {2, 1, 3}]

{{x1, x2}, {x3, x4}, {x9, x10}, {x11, x12}, {x5, x6}, {x7, x8}, {x13, x14}, {x15, x16}}

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