I think there's less climbing on the Harlech road - once you've reached Penrhyndeudraeth the coast road is rolling, whereas the official route from Maentwrog (bus shelter place) to Trawsfynydd is very definitely a solid climb.
Agreed, it's a good old climb, the first year I rode it for reasons completely unknown, I put my head down and pedalled - I dropped everyone in my group, caught the next group. They kept ranting at Dave to do his bit on the front. It became apparent that I was Dave (in fact Dave had dropped back into the group I had been in). So I got on the front and rode away from them as we went over the top and down the hill.
Coast road is a bit longer though.
This might come as a shock, but the coast road will be shorter, not by much - but certainly shorter*.
As to the climbing, the coast road will be flatter in both directions. Surprisingly though, not by much.
A strong southerly or south westerly wind will also make that stretch harder - it is quite exposed in some areas.
Agreed, the coast road is great going north when the naturally prevailing coast winds blow, the biggest hindrance are the cars when you're passing through some of the villages.
If one decided to take the longer option going North, the A470 going north isn't without cars slowing cyclists progress, once you're on the drop passing Trawsfynydd, cars braking will hinder progress.
* assuming you're comparing both of this year's routes up and down between the Penrhyndeudraeth cross and the bottom of the lane from the A493.