Interesting game. Takes a moment to understand, but after checking out a scenario, I have a better understanding of a decent setup. Weave patterns with the lines (with about 3 vehicles per line) work wonders for traffic and happiness. Helicopters are excellent with 4 stations and 2 or 3 choppers as well. Good way to keep everything working like clockwork. I would advise chopper-stations at train stations and ferries, or at least the corners of the city.
EDIT:
Just realized that a radiant star formation from the center of the city outward is the most effective/efficient.
Just transform the central zone into a mass-transit station.
-Choppers have 3 destinations mirroring from center, and extending to the corners. (total 6 stations assigned in bowtie fashion, 3 stops per side |>< | )
-Metros take up the X,Y (0,0) lines, and from those to the corners are trollies going around the perimeter.
-Busses will be dedicated to the 4-square pattern in their respective corner. You can optionally use 1 bus at a time with them moving in figure-8 patterns or 2 moving in a cloverleaf pattern in the corner areas. You can optionally mirror the metro setup, but you may need more busses per dedicated side.
-Ferries will obviously take on the water zones, usually used as an auxillary means of ferrying people along the river areas.
Overall, it should be cheap enough to produce, should yield a decent income, and if unfinished initially, can be constructed/continued swiftly. You can eventually beef up the quality to luxury if you can afford to to amp up usage. I would advise starting with metros and choppers and then trolies to unite them. 3 stops each method (5 for the metros if you want), no more, no less. Busses are a different matter. Go nuts with those.