FWIW, the current stable RouterOS allows MTU of 2290 with wifiwave2 (renamed wifi-qcom-XXX in 7.13). But there totally was a bug that 1500 was the L2MTU in wifiwave2 — even though it allow setting higher. See http://forum.mikrotik.com/t/using-wifiwave2-to-bridge-two-audience-wirelessly-thoughts-4-address-mode/153357/1
But EoIP MTU would have gotten crushed over wifiwave2 until a few months ago… but shouldn’t in recent builds.