Hows old Mombasa a run down sector of New Mombasa'? It was Mombasa. then they built 'New Mombasa' in the artificial island probably so not to spend loads of cash on Demolishion. this makes 2 cities.

That's not right.
Take a look at this satellite map. Today, most of Mombasa is on the island, while urban sprawl carries on for a bit on the mainland. The island-city is pretty modern by African standards, with paved roads and office buildings and factories and parks. The mainland, on the other hand, is much more ramshackle: dirt roads, tin-roofed shacks, lots of garbage and poverty, etc.
The city seen in the game is basically this, but bumped up a notch. The island-city, New Mombasa, is full of massive skyscrapers and gleaming maglev trains and a space elevator. The mainland, meanwhile, is more advanced than it is today, but still a slum by the standards of 2552. Regular paved roads instead of metal ones, dusty office buildings and apartment blocks instead of mega-towers.
So basically, while going from present day to 2552, the modern-day cityscape on Mombasa Island turned into the towering futuristic supercity of New Mombasa, while the shantytown on the mainland turned into a modern-day cityscape that is, by the time of 2552, a creaking and ancient slum, which is thus dubbed Old Mombasa.
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