Deciding on lithium battery chemistry, lithium ion (protected) or Lithium Iron Phosphate (no protection) Safety is critical
Let's start with a very important point: With Lithium based batteries a thermistor is a nice last line of defence, but you seem to be making it the centre point of your thoughts.

If your thermistor triggers on a Lithium based battery, purely from charging, you might want to hook that up to an airhorn so you know to start running.

Do not get me wrong: I fully support having a thermistor in everything that's to do with bucket-loads of energy. But with Lithium based batteries, that's not the be-all and end-all of safety it was with NiCd/NiMH.

Hyperbole aside, if a Lithium based battery is hot enough to trigger a charging chip's thermal limits, your batteries are already being destroyed. If you want a safe consumer product, regardless the type of lithium, you need the appropriate charging scheme.

If you want it to be a quality product, just assembling a pack from protected cells is going to get you into trouble. While individual cells will likely not get damaged during its operational life, the operational life will probably be limited.

When an individual cell goes into protection it will open up the chain, where the other batteries are still "active". There's a number of scenarios when a manufacturer uses single-cell-spec'ed MOSFETs in the protection that will not turn out great for your batteries or their service life.

So, if you want to be taking yourself seriously, you need to build the pack properly, with the appropriate protection board. If you want to be actually safe, with a separate pack wired into electronics, this protection needs to be inside the pack to prevent damaged wires from causing short-currents.

This putting either choice on level ground, since protection boards can be had for your voltages for either chemistry, you need to weigh the advantages and disadvantages of each chemistry against your individual needs.

LiFePO4 will be much safer from self-combustion, even when hard-shorted, but not holy! They are still a bear you should not be intentionally poking. Although there's videos out there showing the pneumatic insertion of a nine-inch nail into well built, branded LiFePO4 cells with no fallout.

LiFePO4 also is much more resistant to formation of so-called dendrites on its lithium electrode, causing it to be less sensitive to short term or low-grade over-voltage.

On the other hand, LiFePO4 in most cases has no more than 3C discharge allowance and is usually advised at 0.5C charge currents. Of course, in Lithium-CobaltOxide based batteries ("Li-Ion") the very high discharge types will always still have significantly reduced life at these currents.

LiFePO4 is more expensive (at the moment) and has a lower storage density (for now) and identifying the right manufacturer in the more affordable cells can still be difficult. The fact that destroying such a cell is harder to begin with makes that even harder when samples are sent. That is, the grey area is much thinner, and if you test samples it's that grey area where your data points live.

However, the reason I stock shitloads of quality LiFePO4 and that they are used in high-end automotive, is that they have clear advantages, even if you need a much higher capacity to get the same high currents;  


They have a lower self-discharge rate
They are a little less affected by residing in high or low charge states
They can be safely discharged below freezing (a major point for automotive)
They contain a somewhat reasonable amount of remaining energy below freezing, 45~80% for LiFePO4, versus 0~35% for most LiIon. Where the exact number depends on the temperature.
They have a relatively level discharge curve for the majority of the energy content.
Minor: Their voltage levels are compatible with many ARM type controllers.


All that said, I see you mention balancing nowhere. This also is less of a task with LiFePO4, but some plan for keeping the cells balanced should still be considered. Whether you bottom-balance, top-balance, full-balance, or active-balance that's your choice. For either chemistry. Or not balance at all, but again, usable life will be reduced noticeably.