Assuming they don't ban the game in MY, then i think the potential outlets could be McD, Starbucks, 7-11, mynews etc.

McD's in MY should have the highest chance of being appointed as those gyms since Japan started the strategic partnership on a big scale. So I will be surprised if McD senior mgmt don't capitalise on this at a global level.

And I don't think the real estate price will shoot up over Pokemon. More of the businesses around that area might grow a lil. This Pokemon thingy is just a phase. Give it a few years, another game will supercede Pokemon and the whole cycle/craze continues all over again.

Based on your points...
The sky is the limit on how they want to go about with this "gym" business.

Apart from using the convenient stores or fast food restaurants like what we just discussed.
Others potential places could be like KTM, MRT, LRT stations or even inside the trains.
Telco's and Petrol Stations can also participate if they want to. Even specific stores or allocated shops in some of the REITS could also capitalise on this.

The above theme seems to be more on "convenience" whereby any person on the move can get access to this gyms anywhere and everywhere.

But, I'm also keen to know whether this Gym thingy can further evolve (e.g higher level gyms = special/exclusive cafes or outlets which are not so common can take part). This would be ideal for those major tourist spots (e.g Sunway Resort, KLCC, BTS, Langkawi resort, Museum Negara) to capitalise on this.

But as usual, potential is one thing, whether worth the $$$ and sustainable is another.