As a rule - the sharper the monitor, the more noticable the scanlines are going to be.
You COULD adjust the focus and bring it out slightly to make the image fuzzier which will reduce the harsh effect of the scanlines... OR, you could try some scanline effects and see how they look (I like 50% scanlines myself). I use that with the multisyncs and am generally pleased though the scanlines may look a bit off to someone analyzing an image.
I don't know if the AVGA will allow you to double up on the resolutions / prescale the image while preserving the proper refresh and such. Advancemame was my fav and didn't even require an AVGA but that build as been discontinued since .106 so the AVGA may be the way to go now.