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The formation and migration of austenite-martensite interfaces plays the key role in reversible martensitic transformations of shape memory alloys (SMAs). How these interfaces interact with the SMA microstructure is a primary determining factor in important functional properties such as hysteresis and transformation span. As such, successful microstructural engineering of SMAs requires in-depth knowledge of interface behavior. The rapid nature of martensitic transformations makes experimental observations of moving austenite-martensite interfaces challenging. Molecular dynamics (MD) simulation is a unique tool which can probe the atomic-scale details of austenite-martensite interfaces as they migrate through different microstructures. However, in focusing on the entire transformation process, including the nucleation of new phases, MD studies are usually performed so far from equilibrium that their relevance to experiment is questionable. Here, we demonstrate new MD techniques to generate energetically preferred austenite-martensite interfaces in NiTi under near-equilibrium conditions. The interfaces are semi-coherent, exhibiting a series of structural disconnections, and they can migrate rapidly through single crystals under only small thermodynamic driving forces. In contrast, when interfaces migrate in polycrystals, their motion is impeded by thermoelastic effects as well as changes in orientation relationships at grain boundaries. Microstructures which accumulate large amounts of elastic energy tend to release some fraction through irreversible, hysteresis-inducing mechanisms. We demonstrate that engineering microstructures with less constraints is a viable strategy to produce SMAs with reduced hysteresis and transformation span. Similar thermoelastic and hysteresis-inducing mechanisms also arise when austenite-martensite interfaces encounter precipitates and can be controlled by tuning characteristics of the precipitate distribution.