Panel estimation has more estimation options and techniques available
As well as specialised panel-estimation techniques for least-squares, two-stage least squares and GMM (including dynamic panel data estimation), most of the standard non-panel estimation methods (probit, liml, quantile regression, etc...) are available on the stacked data. Further any lags/leads will never cross seams (the last observation for one cross-section will never be included in the lags of the next cross-section).
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