Can You run two 2, 20amp Ground fault circuits using 12/3 wire and duplex 20amp plugins
Nope, does not work because you would need a fourth wire past the GFCI to carry protected neutral along with protected hot.  You cannot share unprotected neutral and protected neutral on the same wire.  This problem defeats the purpose of a Multi-Wire Branch Circuit, which is the formal name of what you're trying to do). 

It is a big part of the reason MWBCs are a time-lost wiring method. 

Also, you can't use 2 breakers because you must provide a method to assure that they are on opposite poles (otherwise you overload the neutral) and you must have common maintenance shutoff (impossible to turn one off without the other).  That basically compels you to use a 2-pole breaker.  

Also, there are no tabs to break off on a GFCI. 

I want to do it anyway, and AFCIs are not required here

In that case you can use a 2-pole GFCI breaker, and wire the MWBC in the classic style.  Remember you must pigtail neutral wires to every device, so the device can be removed without interrupting neutral.  

Alternately, you can wire it with a 2-pole breaker without a GFCI breaker, use GFCI receptacles, and not use the LOAD terminals at all.  This moots the issue with the neutral since it is now non-protected neutral in all locations.  

I strongly recommend not using the LOAD terminals unless you are very sure of what you're doing, this causes more trouble than it's worth.  While it is slick when you can do it, the savings of avoiding a few GFCI receptacles is wasted when you have to spend $150 to call out an electrician to make it all work. 

I need AFCI, though

AFCI protection must be at the breaker.  A 2-pole AFCI  is available, but no such thing as a 2-pole AFCI/GFCI breaker. So you would need to exit the panel and stop in a junction box, and fit a 2-pole GFCI-only device (deadfront) there.  

One extreme option there is to come off the service panel to a hot tub subpanel, which has a GFCI master breaker.  Then fit as many AFCI breakers as you need for the various circuits that need GFCI.  Of course, one ground fault would trip them all, so don't put GFCI on the fridge but that is good advice regardless.   

I am willing to use /4 cable downstream of the first GFCI

Actually, you need /2/2 cable.  In that case the wiring is fairly straightforward: white is black's partner neutral.  Red and white-red are GFCI-protected.

At the first box, you pigtail neutral to the GFCI Line neutral.  Supply Red goes to GFCI Line hot.   In the /4 cable, red and white-red go to GFCI LOAD.  Down the line, the two neutrals can't touch each other.  

In the second box, supply black and white go to the GFCI Line inputs, no pigtailing needed here.  Then downline black and white go to GFCI Load outputs.   At this point black/white are one Protected pair, and red/whitered are the other. 

At the third and subsequent outlets, you can split the outlets but must break off BOTH tabs and either pigtail all 4 wires, or use the $3 Leviton Pro outlets that provide screw-and-clamp for 2 wires per screw.  Do not put one on the screw and one in the backstab, because backstabs are not reliable.  

Also use deep/large boxes, because you'll have 8 wires + 1 yoke + clamps + ground for 12 units of fill, so 27 cubic inches of box space.