Bealine,
I think the online check-in facility is excellent, getting that window seat on an exit row, and more generally, how easy it was to check in and go through the airport, made a recent trip to FRA and back with BA much more pleasant.
Are these people changing both seats in one visit to the web site? I don't think the software should allow more than one seat per booking to be specified, the others should be allocated nearby automatically. If checking-in separately, it could be made so that only the first person to check-in gets to choose.
Just this once, I know a bit about the subject
, as my day job involves a railway seat reservation system. Many of these, including the one I write software for, are based on airline systems. Most are clever enough to put groups together, but do seem to have a habit of squashing everyone down one end of a coach.