I went back and re-read the original text:
The Droid Factory waves is currently planned to include 30 figures in 2008, each with an additional piece that together will create one big droid.
So my theory about a series of droids for every wave seems to have been shot down. At least by the original report. So I started thinking again about BIG DROIDS. Here are the ones that come to mind:
This one caught my eye right off the bat. It's the
SRT autonomous short-range transport. You would probably recall it from the Geonosis droid factory, as C-3PO falls and is caught by this self-same droid. An AOTC C-3PO would be an interesting add-in to this particular droid. The fact that this droid is found IN the Geonosis Droid Factory leads me to believe that this could be our prime candidate.

And there are a few large droids that I could think of from
REVENGE OF THE SITH. One is the
IW-37 pincer-loader droid. It made the ROTS visual dictionary, but it didn't really get any screentime in
REVENGE OF THE SITH.

And another is the
CLL-M2 ordnance lifter. Again, it was in the visual dictionary but I don't think I saw one in ROTS.

Another possibility are some of the Seperatist Droids.
First there's the
Heavy Missile Platform or as it's more commonly known, the Droid Gunship.

Next is the previously mentioned
Homing Spider Droid. It's definitely a large droid, and I know that a good number of collectors have been calling for one since 2002. But I think it might be a better fit in the Assault Vehicle line. Nevertheless, here's an image.

And there's also the
Droid tank. Again, this seems more likely as an offering in the assault vehicles line.

As far as large OT droids, I think there are only a few candidates.
Here's one of the
Binary Load Lifters that C-3PO mentions but we never saw in the movies.

There's the
Imperial Probe Droid, but I'm not sure how likely that is given the fact that we already have one.

Those are really all of the large droids that I can think of. So I think these might be some of the options we have in this particular case.