Merging two files, one column at a time

Something like this? Worked with your sample data:

paste  file{1,2} | awk '{for (i=1;i<=NF/2; i++){printf "%s:%s\t",$i,$(NF/2+i)};printf "\n"}'
1/0:3   0/0:5   0/0:2
0/0:1   1/1:7   0/0:10
1/1:3   0/1:4   0/0:3

awk '{
    getline f2 < "file2"
    split(f2, a)
    for (i=1; i<=NF; i++) 
        printf "%s:%s\t", $i, a[i]
    print ""
}' file1

A slightly different approach:

paste -d: <(xargs -n1 <file1) <(xargs -n1 <file2) | xargs -n 3