Except for money saving is there any reason why you would not put 20 amp wiring and 20 amp GFCI receptacle (=1 per circuit) everywhere?
I realize that most folks think with their wallets and not much further, but #12 wire contains 59% more copper than #14 (source). That's (nominally) 59% more energy wasted and pollution created in mining, 59% more chemical pollution from refinement, and 59% more weight to lug around as you work.
It's also much less pleasant to work with in a box, and fills boxes and nuts much quicker in terms of legal capacities.
Using 12AWG everywhere is exactly what I do. As far as waste of materials, the real waste would be owning twice as many spools of wire, everything in two sizes, the money tied up, the wire just sitting around, all that manufacturing totally unnecessary. Grabbing the wrong spool and inadvertently doing unsafe work, etc. And for what? So you can have more nuisance trips, and prevent people from using 20A appliances?
Oh, there's another neat trick I can do. If I have to cram more than 9 wires into a conduit, I can just do it, and use 15A breakers to comply with the conduit fill rules. Other than that I don't stock 15A breakers.
As far as GFCI outlets everywhere, just use one GFCI per circuit, using the LOAD terminals correctly. For circuits where you don't want load X knocking out load Y, it's fine to split the circuit before the "LINE" terminals, so you have two GFCIs protecting two separate zones on the same circuit. Just don't wire them nose to tail or you'll play a "Yo Dawg" joke on yourself.
It seems you have poked a hornet's nest.
I use and advocate 20 amp circuits for receptacles and 15 amps for lighting.
Recently, with LED lighting, lighting circuits draw much less than they used to. 15 amps is usually plenty.
20 amp receptacles are not required on 20 amp circuits unless you have a very high current draw piece of equipment.
The only cost difference is the wire.
As others have said #12 solid is more difficult to work with in switch boxes but it is worth it for receptacle circuits because of the extra ampacity.
Is there a reason not to use 12 other than cost. Waste has been raised as a possibility. I have found the need to replace a lot of #14 wire in the past but rarely need to replace #12 an AC unit is the one place that I have needed to upgrade #12. I have wired several homes with #10 (what the owner specified). To try and answer the question I would say wiring with all # 12 and not using 14 is fine and done on many high end homes as a selling feature. To answer the GFCI question only 1 is needed to protect the entire circuit, multiple GFCI'S may cause false trips I have seen this more than a few times. Since the question has been updated I will add that multiple GFCI's can cause false trips especially when testing a device that is fed from a GFCI.
I believe it's a preference. Originally (1960's) there were only three required 20A circuits in a single family dwelling. 2 small appliance and 1 washer receptacles. Over time other circuits are added 1 for bathrooms, we always installed a 20A for the newer microwave due to increased loads, also larger and more sophisticated dishwashers, disposals and refrigerators. So you may wind up with 6 or 7 20A breakers. Now most of the work I have done in the past is commercial and industrial so we always run a 20A circuit as minimum. Any house I have done were strictly high value custom homes so we always just installed 20A circuits. And I am not really interested in any arguments whether it is right or wrong.
On the second part of your question. There is really no need to run GFCI circuits throughout the whole house since the 2014 NEC now requires all outlets to be AFCI protected anyway. There are differences between Ground Fault and Arc Fault but both are used to prevent shock and burn hazards. So at this time the idea of extra protection by adding GFCI's is not necessary. Just follow the NEC on new construction or upgrade to the most recent NEC.