Re: how to fix setup time violation after synthesis, don't lower the operating freque
First the setup must be met after the synthesis.
You could constraints the synthesis with higher frequency, to force it to choose better architecture for speed, and then relax the setup constraint during the PnR.
To obtain a better synthesis you could also used the synthesis with physical or topological information, which help to estimate the net delay.
During the synthesis, after placement you shouldhave the setup met, with a optimization design phase, and so on after CTS and after routing, and for si mode as well.