May  be, in the past that was something that helped me, you should check your 
startup-logfiles for messages that indicate problems with the graphic driver. I 
am not expert, so I can not tell you exactly what I did, but it turned out that 
Ubuntu used a fall back graphics driver instead of the real one, which caused 
the system to be slower and also caused the overheating. I can not remember 
exactly, but in one Ubuntu version I googled the error message and found 
instructions to fix it. In another version I just learned about the 
xorg-edgers-ppa with the newest versions of graphic drivers (and also fresh 
kernels). That helped very much and I am running them ever since (but on my 
x201 I do not have over heating without xorg-edgers)
You may also check, if your system is using Thinkpad-ACPI instead of ACPI. This 
should happen automatically. Otherwise you need to enforce it on system 
startup. Do not ask me exactly where, just google it, that was what I did.

What also helps temporarily: Remove the battery if you work on AC.

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https://bugs.launchpad.net/bugs/751689

Title:
  ThinkPads overheat due to slow fans when on 'auto'

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