flannel is a looser weave fabric than the regular cottons we quilt with- making it even easier to sew- so embroidery is quite easy on flannel- as is applique, quilting, any needle work
as for your other questions- it all depends-
do you want it to be a little baby quilt? some are made about 30" x 40" (or about the size of a yard of fabric)
do you want it to be a bit larger- like a crib quilt- something to last a bit longer? a good size is about 42" x 54"
block size should be (complimentary to the size chosen) if a small one 4"-5" blocks are good- if larger 6"-8" work well- depends on what you choose to do-
as for batting- polyester holds up well for lots of washings & makes nice (kids) quilts---there are some who will say 100% cotton all the way---it's up to you- if you want it to be kind of puffy/lofty poly batting is a good choice- if you want it more-flat- cotton like warm & natural works fine.