I do some pretty serious trainer work on weekdays - am building for my first half ironman triathlon, which requires a fair amount of biking on the plan I"m on.
I've been using bike trainer distance. Some say that the only metric is "time spent in HR zone" but I'm finding that since the bulk of my training is aerobic longer-distance style riding since there's no drafting in triathlon, tracking distance is best for me. If I just go by time, I can be off by as much as 1.5 miles by the end of a 25 mile trainer ride depending on subjective effort. By tracking the distance, it's a pretty honest effort.
I will soon however be entering my 'speed' phase of training where I do dedicated speedwork interval workouts. On those workouts, the metric for me changes completely to my speed/HR during the interval, and not the overall average or total, since the hard effort is what counts, not the rest.
I agree with Merlin's view on the miles ridden not mattering for outdoor rides of varying terrain (I go from 20+ on flats to 14 on super hilly routes for same effort), but on a trainer where everything's stable, more miles = more total work. Doesn't mean the intensity is the same of course (intervals duh) but for total work performed on a trainer, more miles = more work done. Even if the work is done at an overall easier power rate.