This question pops up from time to time.
Every now and then, some functions are redesigned. Of course not all functions would be re-designed every release, but I would imagine that some functions get an overhaul more often than others. This is done to improve the speed, and/or precision, and/or flexibility of the function. For some specific use cases this will result in much slower code, even if on average everybody's code performance might improve.
Sometimes a lot of things get a major overhaul. The last time this happened very prominently was with R2014b, where the internal design of graphics elements was changed. This resulted in a wealth of new possibilities, and a lot of old code breaking (although that would in general only happen for undocumented uses).
The only real answer is: enjoy the release that works fastest, and use the debugging tool and the profiler to get a better look at the bottlenecks.
If you want help on a specific situation, you should post more details.
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