I don't pretend to be a battery expert, but from the research I've done the Li-Ion is more stable and less likely to cause fires if slightly mis-handled or damaged than the Li-Poly. However the Li-Ion does not have the discharge rate capability of the Li-Poly which is why you find them in electric powered applications.
So I use Li-Ion for rx/ignition on my latest model and Li-Poly on my foamies which are the only electric powered stuff I have.
There is a new chemistry of Lithium/Manganese coming out, although they are somewhat limited in sizes and availability right now, which has the promise of the discharge rates of Li-Poly without the hazards as it's not the volatile chemical combination of the Li-Poly's.
Duralite has the new stuff, but not much information about them is posted;
http://www.duralitebatteries.com/batteries-mg.html