Atkins (gigantic international engineering and design consultants) drew up the plans - their logo is plastered all over the maps. Sustrans might part fund the project, but have not had anything to do with the design that I am aware of.
It would be fairly tricky to plan a direct arterial cycle route from the west of the city that didn't get pretty close to Haymarket. Anyway, why would you avoid it (from a design point of view - nice to actually avoid the hellish traffic/tramline maelstrom). It's a major trip attractor. The whole point of these new city centre lanes is they go where people actually want to travel.