Charterhouse's campus is very open - would be more difficult in terms of security. Wellington has a reputation (unfairly or not) for being 'flashy' and full of celebrities' kids - I doubt that would appeal to William and Kate. I suspect they will opt for co-ed, although clearly Eton is under serious consideration.
Marlborough is only an hour's drive from Windsor and 45 mins from Kate's family in Bucklebury, plus Eugenie went there so there's a precedent of them being able to logistically accommodate royal children. William and Kate are also big users of the royal helicopter, including when they travel privately between their homes (I'm not a fan, but anyway...) so that would further cut down on journey times.