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It has been claimed that the standard model of cosmology (LCDM) cannot easily account for a number of observations on relatively small scales, motivating extensions to the standard model. Here we introduce a new suite of cosmological simulations that systematically explores three plausible extensions: warm dark matter, self-interacting dark matter, and a running of the scalar spectral index of density fluctuations. Current observational constraints are used to specify the additional parameters that come with these extensions. We examine a large range of observable metrics on small scales, including the halo mass function, density and circular velocity profiles, the abundance of satellite subhaloes, and halo concentrations. For any given metric, significant degeneracies can be present between the extensions. In detail, however, the different extensions have quantitatively distinct mass and radial dependencies, suggesting that a multi-probe approach over a range of scales can be used to break the degeneracies. We also demonstrate that the relative effects on the radial density profiles in the different extensions (compared to the standard model) are converged down to significantly smaller radii than are the absolute profiles. We compare the derived cosmological trends with the impact of baryonic physics using the EAGLE and ARTEMIS simulations. Significant degeneracies are also present between baryonic physics and cosmological variations (with both having similar magnitude effects on some observables). Given the inherent uncertainties both in the modelling of galaxy formation physics and extensions to LCDM, a systematic and simultaneous exploration of both is strongly warranted.