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Transmission electron microscopy (TEM), and its counterpart, scanning TEM (STEM), are powerful materials characterization tools capable of probing crystal structure, composition, charge distribution, electronic structure, and bonding down to the atomic scale. Recent (S)TEM instrumentation developments such as electron beam aberration-correction as well as faster and more efficient signal detection systems have given rise to new and more powerful experimental methods, some of which (e.g., 4D-STEM, spectrum-imaging, in situ/operando (S)TEM)) facilitate the capture of high-dimensional datasets that contain spatially-resolved structural, spectroscopic, time- and/or stimulus-dependent information across the sub-angstrom to several micrometer length scale. Thus, through the variety of analysis methods available in the modern (S)TEM and its continual development towards high-dimensional data capture, it is well-suited to the challenge of characterizing isometric mixed-metal oxides such as pyrochlores, fluorites, and other complex oxides that reside on a continuum of chemical and spatial ordering. In this review, we present a suite of imaging and diffraction (S)TEM techniques that are uniquely suited to probe the many types, length-scales, and degrees of disorder in complex oxides, with a focus on disorder common to pyrochlores, fluorites and the expansive library of intermediate structures they may adopt. The application of these techniques to various complex oxides will be reviewed to demonstrate their capabilities and limitations in resolving the continuum of structural and chemical ordering in these systems.