That came up recently. EIP-615 won’t start out as breaking change, but might become one, and I’m not wanting to solve the versioning problem in general before moving ahead. Discussion here, including list of 7 or 8 active versioning proposals.
Wasm could be a completely separate VM, or could be integrated more or less tightly to the EVM, (e.g. as literally the assembly language that the EVM compiles to). But we’ll need an EIP for eWasm to discuss this in much detail.