I rode Route 3 from BA to Ushuaia a month beck and am now heading north along Route 40 / Carretera Austral. Knowing what I know now (and if you have a spare US$500 or so), I would recommend:
BA to Mendoza; south along Route 40 to Bariloche; cross into Chile to Puerto Montt; take the Navimag ferry to Puerto Natales (about 3 days): then north up the 40 back to Bariloche (with the option of driving the Carretera Austral); and then back into Chile and to Santiago. It's effectively a figure of 8 loop, so you don't cover the same ground twice - and you get to ride a lot of Route 40 as well as heading up the Chilean side between Puerto Montt and Santiago.
This route has 2 big advantages: you avoid a very boring and long drive down Route 3 (flat, straight, nothing really to visit except Puerto Madryn); and the ferry ride down through the hundreds of islands is meant to be awesome - if the weather isn't foggy. The downside is the ferry isn't cheap.
IMHO Ushuaia isn't really worth the extra mileage.
Bits of the 40 are still gravel and dirt, but learning to ride on it will be part of the adventure; I dropped my bike about 10 times one day when Route 40 turned to mud and ended up hitching a ride in the back of a 4X4 pickup when the road became impassable - and it was the most fun day of the trip so far! And to get the most out of this part of the world, you need to ride some gravel. (The Carretera Austral is a wonderful road but most of it dirt.) I suspect this applies up north too.
Patagonia will NOT disappoint - but be prepared for the touristy bits like Torres Del Paine, Calefate, El Chalten.
Can't comment on the northern loop - haven't got there yet!
Hope this helps.
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