I have a hard time imagining how any city building game can have an engaging multiplayer mode. Tropico 5 might have one that works - if for no other reason than that you can wage war on your playmate should you grow tired of cooperating.
For Skylines, the only way I see it happening is if all interaction is effectively 'off map'. That'd limit it to cargo trucks and cims moving between the cities using the outside city connections, maybe negotiated service capacity treaties for water/power/garbage/corpses, options for preferred trading partner (so more trucks go that specific highway route), etc. Maybe have Chirpee supply information between the cities, in form of rivalry/friendship messages and suchlike. Something like that might be feasible within Skylines' lifetime. Two players on the same map, not so much.
For that matter, sharing the same map doesn't sound the slightest bit appealing to me, even with the tile purchase model mentioned in this thread. All that'd do is make you see what your friend is building. It wouldn't be direct interaction, it'd just be a race to the best tiles.
Come to think of it - having an "MP mode" where Chirpee shared the status of your Steam friends' cities might be interesting. No interaction, of course, but still; "Mayor Bill55 has grown Farmityville up to five thousand citizens. Citizens of Springburg are in awe, and begs the mayor to promote growth."