The Highland Railway regarded Inverness as their territory and vigorously blocked any schemes that even hinted at encroachment. They even considered building down the Great Glen to Fort William to prevent any opposition railways getting into Inverness, except that the North British were equally resolute about anybody else getting into Fort William.
The independently proposed Fort Augustus branch, as the first stage of a line up the Great Glen, threatened to destabilise this delicate balance. Predictably, the Highland viewed the line with alarm, trying everything to block construction and financially ruining the company before construction started. When this failed, they outbid the North British to operate the branch, leading to the anomalous situation of a Highland Railway operated branch physically separate from the main system. This anomaly continued for a few years until it was obvious that the Fort Augustus branch was an over-engineered financial disaster and going nowhere, at which point the Highland lost interest.
Were it not the byzantine manoeuvrings of Victorian railway companies, I am sure there would be a line up the Great Glen and, bearing in mind the Loch Ness tourist trap, would be doing very well. However, that is history for you ...