Ok, first let’s talk about a bit of history. ‘WebParts’ was born when WSS 2.0 was first introduced. In ASP.NET 2.0 framework new version of ‘WebPart’ was built which can run with out WSS. WSS 3.0 uses the ASP.NET 2.0 ‘WebPart’ framework.
So some quick points:-
So the decision will be more based on what level of back ward compatibility you are looking for.
Below sheet shows the new WebPart classes as compared to SharePoint Backward compatible class.

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