I think that Merle will come back around, possibly in the next season, or whenever they come in contact with the Governor arch.
I think that because they wouldn't have put so much detail into how he escaped the roof-top in Atlanta, or would have showed him in Chupacabra. But that's just me. sweatdrop
Him I never thought of that pretty interesting though. Merle would fit right in with the other group I think it may be possible. But apart of me thinks we may never actually see the other group.
I think he might show up eventually, but you just never know with this show. He could show up again for 10 minutes then get killed immediately, like Tony in the bar.