I tried your suggested layout of my repo folder:

Code:
# ls -R noarch/
noarch/:
my-aix-99.0.0-125_99.0.0-126.noarch.drpm  my-aix-99.0.0-125.noarch.rpm
I then executed:

Code:
# createrepo .
Spawning worker 0 with 1 pkgs
Workers Finished
Gathering worker results

Saving Primary metadata
Saving file lists metadata
Saving other metadata
Code:
# ls repodata/
filelists.xml.gz  other.xml.gz  primary.xml.gz  repomd.xml
Doesn't look like it recognized the delta RPM.
Code:
# zypper se --details my-aix
Loading repository data...
Reading installed packages...

S | Name         | Type    | Version                               | Arch   | Repository
--+--------------+---------+---------------------------------------+--------+-----------
i | my-aix       | package | 99.0.0-125                            | noarch | tr
When I added the --deltas option it created an empty prestodelta.xml.gz. Createrepo does not recognize the delta rpm with this file layout.

FYI: I'm on SLES 11 SP3

So I tried something else. In order to use createrepo --deltas I had to re-arrange my folder layout:

Code:
# ls -R.
.:
drpms  noarch

./drpms:
my-aix-99.0.0-125_99.0.0-126.noarch.drpm

./noarch:
my-aix-99.0.0-125.noarch.rpm

# createrepo --deltas .
Spawning worker 0 with 1 pkgs
Workers Finished
Gathering worker results

Saving Primary metadata
Saving file lists metadata
Saving other metadata
Saving delta metadata

#zcat repodata/prestodelta.xml.gz
<?xml version="1.0" encoding="UTF-8"?>
<prestodelta>
  <newpackage name="my-aix" epoch="0" version="99.0.0" release="126" arch="noarch">
     <delta oldepoch="0" oldversion="99.0.0" oldrelease="125">
      <filename>drpms/my-aix-99.0.0-125_99.0.0-126.noarch.drpm</filename>
      <sequence>my-aix-99.0.0-125-beac8cc49fb8363d0eec60581ed00df59c1110</sequence>
      <size>63681</size>
      <checksum type="sha">5cb36d09b28582fa37a88a066b4c7aea659bc20e</checksum>
     </delta>
     </newpackage>
</prestodelta>
But zypper still does not recognize the deltas.

Code:
# zypper se --details my-aix
Loading repository data...
Reading installed packages...

S | Name         | Type    | Version                               | Arch   | Repository
--+--------------+---------+---------------------------------------+--------+-----------
i | my-aix       | package | 99.0.0-125                            | noarch | tr
Note that createrepo generated a prestodelta.xml.gz.