Two days one night is perfect for Pondi.. however check for rain.. it may be a bit humid in day time but a dip in water can take care of it :)
Humpi is also a good visit for a glimpse of history and architecture.
Without any second thoughts it has to be Pondicherry for 2days. Quite good places to explore, quite a peacefully happening place and an evening by the Mahatma Gandhi beach would be far relaxing then at Hampi.