Since they are all so easy to enable and disable with JGSME, why not try them all? Most of them gives you tons of realism. I myself prefer TMO (Trigger Maru Overhauled) over all other supermods i've tried. Fall of the Rising sunt (FOTRS) is also good, and Run Silend Run Deep (RSRD) is also great. All of them deal with the issue you mentioned (having all historical ports available to reload and refuel), thouhg you can only repair and end mission at your home port. But that is only the tip of the iceberg, SH4 is great with any of those mods (it helps to have 1.5, that meaning 'u-boat missions').
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