Great to hear from CAs interested in implementing ACME!
Just about all client implementations currently target the
acme-01 draft. Boulder, the CA software behind Let’s Encrypt, likely will stick with that version of ACME until the IETF finishes the standardization process (though there are a few backwards-compatible things from later drafts that are supported by boulder).
I’d say if your plan is to be compatible with most ACME clients for the next 12 months or so,
acme-01 should be your target, though my guess would be that most clients will track Let’s Encrypt and switch to the new version of the protocol once Let’s Encrypt offers it, so you might have to follow suit.