Does suface area affect thermal coupling design?
Thermopiles are not well suited to generating large amounts of current, typically only a few tens of milliamps. They also do not generate much voltage per thermocouple hence you have to put them in series to boost the voltage. even with this you need to generate the highest possible thermal difference from couple to couple to get anything out of them. Still it would be possible to generate enough to power low wattage loads. You could buy a thermoelectric cooler module and clamp it between a cold plate and a hot plate and it would generate some power at its leads. Those devices would be optimum for many applications. Don't expect to get much out of a string of thermocouple wires all twisted together though. The short answer is to improve the thermal coupling to the junction itself.