As you say you want to play games on it then you deffinitly want to go with the A4000 as there's no way of getting AGA to run on the A3000. It's simple as that.
Some might dissagree but I think the A4000 has a much better design than the A3000. Ok it's a bit taller but that makes room for the 5.25" unit witch is a must have (who has a machine without CD these days? want to have that in a box next to the machine?). It also proves to have better airflow so should be gentlier on demanding accelrators.
It does lack internal SCSI, true, and most accelrators can correct that and SCSI zorro cards can be found fo almost nothing so it's realy not an issues.
It does lack the scandoubler flickerfixer and that's probably the biggest setback as it can be hard to find. However, untill you do, why not run a 2 monitor system (1084 are also found for almost nothing)?
For graphiccard I'd say either a PIV or CV64 / CV64-3D. But personaly I think you should get a mediator and a Voodoo3 right away.