The systems we have for voting in Washington DC seem to be a best-of-both-worlds approach. There are touchscreen kiosks that you use to make your choices, then the kiosk prints out a properly marked paper ballot that it asks you to verify. Then you take your ballot over to the normal scanning machines. You can also request an unmarked ballot and fill it by hand if you prefer.
The kiosks can provide a wide range of assistive tech (larger fonts, instructions in a variety of languages, and headphone jack for audio prompts). They also help ensure you do not miss a question - you must explicitly choose "skip" - and they help ensure you select between 0 and N choices in choose-N questions. Also they print a clearly-marked ballot which helps avoid ambiguities like if somebody partially fills a circle by hand.
And best of all, the end product is still a physical, auditable piece of paper.