TPS61200 gets really hot
In looking at your layout, you don't have a great thermal ground connection and are doubling your thermal resistance (Junction-to-board characterization parameter 16.8 C/W, if I read right which also happens to be the lowest thermal resistance pathway to the ambient) to the ground plane by halving the connections to it. And not having as much ground plane to sink current also presents an issue. The layout guideline in the datasheet has the ground connected on both sides. A quick look to the datasheet also suggests as well as other issues with this design: 


  If the layout is not carefully done, the regulator could show
  stability problems as well as EMI problems. Therefore, use wide and
  short traces for the main current path and for the power ground
  tracks. The input and output capacitor, as well as the inductor should
  be placed as close as possible to the IC. Use a common ground node for
  power ground and a different one for control ground to minimize the
  effects of ground noise. Connect these ground nodes at any place close
  to one of the ground pins of the IC.


It also looks like the inductor is located far away from the IC which probably isn't that big of a deal, but the cap C11 could be a big issue. You have a small trace from the battery to the power cap and from the power cap to the TPS61200, these traces have parasitic resistance and inductance. This parasitic impedance blocks the effectiveness of C11 and also makes it harder to source power from the battery at high frequencies. At this point I would consider scrapping this design and making it more like the manufacturers suggestion. 

You could run through the power equations and throw in parasitic resistances and inductance and see what your biggest source of thermal error is. Simulating it in spice always helps too, and the parasitic resistances and inductances can be calculated from PCB trace calculators.  One thing that you could do is beef up the traces to C11 with a blue wire and see if this helps on your current design.

Short story, follow the manufacturers lead on these, or do lots of math, but it usually takes less design time to just go with the manufacturers tested solution. Sometimes you can get away with layouts like this if your not generating a lot of heat in the switcher.