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Three things act to mitigate any increase in parasitic C caused by increased width in higher metal layers:
1) Higher level metal layers also tend to be thicker, not only wider. So cross-section increases (reduces R) on the order of "n^2", while surface area increases (increases C) on the order...
primetime report_timing exceptions
Most timing tools will have some report that tells you if path endpoints are unconstrained. For example, the Primetime "check_timing" command can report this. Magma and Cadence tools also have similar functionality.
What EDA tools are you using to check...
Re: Does Latency is more important or Skew is more important
As others have said, it does depend greatly on your individual application. But a good rule of thumb to help you decide which is more important to your design is that synchronous interface timing depends more strongly on latency...
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