I've read, but have no evidence of it otherwise, that running these generators in 240v and uneven loads on the two legs can cause the voltage to be a little different on the two legs (like 130v on one and 110v on the other). If that's the case, is it an issue I should worry about?
Not really, as long as you make some effort to balance loads between legs. For example, if you have two air conditioners, put one on each side. The loads do not need to be identical.
1) Leave the generator on 120v, wire it with 6/2 cable, and bridge the black/red on the input of the transfer switch to share power between the two input legs?
That is not an option. If you do end up drawing a full 66 amps, you will overload your 50-amp transfer switch. Also, #6 will be marginal for 66 amps. Remember that even though each of your two existing "hot" legs coming from the generator will be carrying 35 amps or less, when wired for 120, the neutral will be carrying the sum of the total current, or 66 amps. You would need to upsize the transfer switch and the wires to run the unit on 120 at the full 66 amps.
2) Do the above, but replace the generator output breaker to a single 50 amp?
That' an acceptable solution, as it will ensure that the neural current is 50 amps or less. You could also put another panel in between the generator and transfer switch, to make use of the 16 amps you would otherwise leave on the table this way, for example to run an extra batter charger.
3) Go with 240v and hope for the best with the loads on each leg? I haven't checked to see what the draw of the AC units are so I really have no idea if I could run two AC units on one 33 amp leg.
This method allows you to use the full output of the generator, but creates the additional problem of load management. You will not be able to run two ACs per leg, so this would also limit you to two ACs total.
Probably the least expensive solution that provides the most flexibility is to wire the genny for 120 and put a two-position panel between the breaker and the transfer switch. Supply the transfer switch through a 50-amp breaker and add a 15-amp breaker for another dedicated circuit that only works when the generator is running. That will give you a full 50 amps without having to balance loads and without having to replace your transfer switch and hardware.