The ferry will take about an hour longer in moving time to get as far as Broadford and cost about fifty bucks more. Add some more time for whatever lead time you have to check in for the ferry or miss your booking - - it's generally at or less than an hour, but I forget what this one is.
The only road you'd duplicate is the one from Loch Oich to the bridge. It's scenic and looks different depending on the direction.
The road from Fort William to Mallaig is spectacular. A thirty-minute ferry ride isn't that bad.
I'd vary the routes.
When heading toward Inverness, you'll come to the A87/A887 split. Stick with the slightly longer (by all of twenty minutes) A87 for better scenery and the opportunity to stop at Fort Augustus for the staircase locks.
When popping up the hill after Drumnadrochit you'll hit a 'T' intersection. There's a monster museum to the left and one to the right. The one after the right turn with a dragon in a pond is really pretty good and well worth and hour and whatever they stiff you for admittance.