My experience is that the smaller wheel is better. Here's why:
My first E-bike had 28" wheels, because this is the size that I use for a normal bike too. And I though it will be faster than a small wheel. And yes it was fast, at 48V, the max. speed was around 50km/h with a 500W controller. Then I tried a stock 300W E-bike which looks like a scooter, it has 18" wheels and damn, even with the weak stock controller, it had much more torque and had better throttle response, because smaller wheel has better torque. So I started using the E-scooter instead with the 500W controller, it pops wheelie from standstill and from 52V 33Ah, it gets me up to 40km/h in a few seconds. You can still go fast with small wheels and still have great torque if you increase the voltage. I did some test with that E-scooter, I bought a 108V controller, so I was able to test those 18" wheels with 96V. It had impressive torque even with those heavy SLA batteries and the max. speed was 70km/h! The 28" wheel with from 84V got me up to speed 70km/h too, so the voltage was lower, but it was really weak and the motor got warm, because the large wheel is really ineffiecient. If you use ebike.ca's motor calculator, you can find out, at around 75km/h, the larger wheel will actually be slower, when everything else is the same. But the smaller, 16" will be slower too, the optimum is the 20" wheel.
So that's why my new E-bike will use 20" wheels, all suspension frame and a 104V 33Ah battery pack.
Also, higher voltage requires less current, and it will be better for the battery pack and for the cables too. If you double the voltage, you will only need half current to maintain the same speed so you will have a better range.