For getting an idea how the overall Ubuntu Linux performance has evolved over the past two years for those solely riding Long-Term Support releases, I compared the performance of Ubuntu 14.04.0 to Ubuntu 16.04 LTS in its current daily ISO form. The tests were done on the same Intel Xeon E5-2687W v3 (Haswell) system with MSI X99S SLI PLUS motherboard, 16GB of RAM, and AMD FirePro V7900 graphics.
The same components were obviously used for testing these two latest Ubuntu release trains. For this system note that with Ubuntu 14.04 it was on ACPI CPUFreq while under Ubuntu 16.04 the default CPU scaling governor is Intel P-State in the performance mode. Ubuntu 14.04 rode Linux 3.13 while Ubuntu 16.04 is set to finalize on Linux 4.4. There is also the big compiler difference of GCC 4.8.4 vs. GCC 5.3.1.
In the file-system tests there wasn't much difference with all the recent Ubuntu releases riding on the EXT4 file-system.
HPC Challenge? Minimal difference in the out-of-the-box performance.
Some benchmarks sadly seem to indicate regressions along the open-source stack over the past two years.
Others have seen some small gains.
See the rest of these early Ubuntu 14.04 vs. 16.04 LTS benchmarks on the Xeon E5 Haswell system via this OpenBenchmarking.org result file. In case you missed it, also be sure to check out the recent Ubuntu 6.06 to Ubuntu 16.04 LTS benchmarks for a very different system (AMD Opteron).