1 a
2 b
3 c
...
              File2

2 a
2 c
2 d
...

1 a,2 a
1 b,2 c
...

paste -d, File1 File2 | awk -F, '{n=FN/2;s=""; for (i=1;i<=n;i++){printf "%s%s", s, ($i-$(i+n));s=",";}; print ""}'

1 a

1 a