1. Safe chemistry.
2. Holds a higher voltage under load than lithium ion, making for higher brightness over the run. (incans)
3. Slightly lighter weight.
4. Appear to have better performance and less prone to failure in cold weather. (unconfirmed)
5. No PCB on the IMR's to fail or drain the battery.
6. Fits in tight bodies, like the A2 or newer E series more easily. (again, no PCB)
7. The first setup I listed on post #2 of this thread was only possible with lithium cobalt cells because I went through 6 new lithium cobalt RCR123a batteries and was able to find two that fit into my A2's body after peeling the labels. With the lithium manganese (IMR) cells, all six I had fit perfectly just like a CR123a cell. Runtime should actually be improved with the IMR cells, since I'm running a Lumens Factory HO-A2 lamp assembly, which draws more current than the recommended 2C max discharge rate of lithium cobalt cells. I'll have to double check the current draw, but I believe it was over 1.3A.
The second setup I listed is impossible with the lithium cobalt cells as they cannot provide the 1.9A current the EO-9 needs to run.
The third setup will work fine with either type of cell and the lithium cobalts will probably have a slightly longer runtime.
But it's not enough to outweight the negatives, in my opinion.