A versatile group of 2D carbide materials from the past decade, MXenes, have attracted attention for their rich chemistry and wide range of properties. The perhaps best known MXene, namely, Ti3C2Tx, has been observed to stack in two distinct ways, and simulations show that this influences interlayer bonding energy and Li diffusion. In this DFT study, six types of Ti3C2T2 interlayer bonds resulting from O, F, and OH termination groups are assessed with respect to stability. It is shown that OH termination groups are highly stable up to 50% coverage, but unstable for higher coverage. A model to predict stacking type based on termination group chemistry shows that the degree of hydrogen bonding is the deciding factor. The model is also tested on V2CT2 and Zr3C2T2, giving similar results to those of Ti3C2T2. By calculating migration barriers for Ti3C2O2, we show that Li, Na, and Mg have orders of magnitude faster diffusion in the stacking favored by hydrogen bonds. XRD patterns calculated for both stackings show they are close to indistinguishable, highlighting the need for caution when classifying stacking.