I voted for SH4, basically because of all the extra possibilities.
Most things that function in SH3 also function in SH4 (with only rare exceptions like the schnorkel), while many functionalities of SH4 don't work in SH3. For example the extended crew/systems functionality in the .upc files.
SH4 does take a bit longer to mod, because of all these extra functions, but IMO the result is better.
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