When you have two main routes crossing, unless one of them has an increased dwell timetabled for overtaking I think you could normally only have one optimised connecting route. However in this case, going back a fair while, I think the 'reasonable connection' that they have tried to sustain IS that for the Portsmouth/Southampton to Exeter via Yeovil (and vice versa). To the best of my recollection that has usually been the case since the late seventies.
Therefore by default, Waterloo towards Westbury changing at Salisbury (and vice versa) is not the intended priority.
Paul
The problem with the Portsmouth/Southampton to Yeovil/Exeter connection is that the timings are a bit tight (about seven minutes), and passengers have to change platforms. If the train from Portsmouth arrives on time, the connection works well, but it doesn't take much delay to cause problems. And I assume that holding the Exeter train for more than a few minutes is difficult, because of the knock-on effects on the single-track beyond Wilton.
If the timetables could be tweaked to give an extra five minutes between trains, the connection would be more reliable - and it might be possible to make it a same-platform interchange. And passengers making the "other" westbound connection (Waterloo to Westbury) wouldn't have quite so long to wait at Salisbury. But that's easy for me to say - I'm sure that actually doing it would be far from straightforward.
The eastbound connection is much more comfortable - fifteen minutes, and a same-platform or cross-platform interchange.
Steve