You can set “any” vertical resolution (0-1080) in your retroarch.cfg. For example you could set something like 1080/2=540 or 1080/4=270 to get integer scaling. If the aspect ratio of your render resolution differs from your display resolution horizontal resolution will be recalculated. You can try to get the best fit for performance and visual appearence. Render resolution upscaling is for free (hardware). If render and display resolution is equal software integer scaling is used (performance penalty). It is also possible to modify the hardware upscaler to your needs: https://github.com/raspberrypi/firmware/issues/104
As i have said default visual settings are not optimized for rpi2 at the moment. If we find better defaults we can at them.