you can't determine the top speed of either engine unless you know specifically what the rear sprocket size is.
it also depends on how the carb is tuned, what spark plug you are running, the fuel-oil ratio, the rear wheel size, the rear tire size (height), rider weight, bike weight, etc.
You can't just say " a 66 c.c. will top out at 35 mph and a 49 c.c. will top out at 16 mph."
there are a ton of variable that will affect top speed.
you can gear a 32 c.c. engine (for example) to have more top speed than a 66 c.c. engine just by the gear ratio.
more top speed means less bottom end torque and slower take offs.
you can gear one of these enignes either for top speed, or low end torque with a single sprocket.
if you want the best of both worlds then you would have to look into a shift kit.
My 49 c.c. 2 stroke, for example, has more top speed than my 66 c.c. 2 stroke. BUT, my 49 has an expansion chamber, high flow air filter, 41 tooth sprocket, 20" wheels, accell 7mm, spark plug wires, ngk spark plug, 20" schwinn frame, and i weigh 160 pounds. top speed is around 32 mph on that bike with ME riding it.
My friend can get on it, and he weighs 180 pounds and the top speed drops to around 28mph.
My 66 c.c. bike also has 20" rims and a 41 tooth rear sprocket, but it has a 24" tall rear tire(which technically whould give more top speed because it makes the gear ratio slightly higher). but it's an o.c.c. chopper frame which weighs more than my standard stingray. it has a modified long pipe (not an expansion chamber) high flow air filter in a custom made carb stack, accell plug wire and ngk spark plug. the engine has slightly more torque than my 49 c.c., but the bike itself weighs more so the top speed is more around the 30 mph range with me on it.
but again, if my 180 pound friend rides it, top speed drops to around 25-26 mph.
since i own both a 49 c.c. and a 66 c.c. i can tell you that both of my engines are pretty reliable and i haven't had any problems with either of them. (the 49 is 4 years old and the 66 is about 3 years old).
BUT, i do not rely on them for every day transportation and i just ride them for fun.
whatever size engine you buy and whomever you buy it from is a **** shoot.
sometimes you get a good one, sometimes you get a lemon.