I think Straight and Direct Modes still tailor the A speakers to the YPAO equalized process, so if you switch to B speakers, these parameters still apply. Pure Direct mode may solve the problem, but then your subwoofer in this mode will not be activated.
I use the System Memory function to solve the Speaker A/B problem. System Memory Function is readily available on the RX-V2500 on the remote, but you can also access this function on the RX-V1500 through the Extended Remote Codes (go to this web site if youyou want to learn more about it:
http://www.yamaha.com/yec/customer/codes/Yamaha_Project.pdf)
Basically I had the YPAO calibrate my Speaker A setup, then I save it in System Memory 1. Then I switch to Speaker B setup and manually defeat all the YPAO calibrations (setting distances to 0, levels to 0, channels to Stereo, etc.) and save this setting to System Memory 2.
So it will be a matter of switching between System Memory 1 and 2 to listen to Speaker A in YPAO and Speaker B in unequalized stereo mode.
Good luck.