We ended up switching our itinerary around a bit, but here's what we did for our trip:
Dec 13th arrived Bangalore, Hotel: Royal Orchid Central
Dec 16th day trip to Mysore, overnight train to Hampi
Dec 17th Hampi, overnight train back to Bangalore
Dec 22nd flew 9W to Cochin, Hotel: Hilton Trident
Dec 23rd Cochin, Hotel: Hilton Trident
Dec 24th drove to Alleppey, Hotel: overnight houseboat
Dec 25th Kumarakom, Hotel: Backwater Retreat ()
Dec 26th drove to Thekkady, Hotel: Taj Garden Retreat
Dec 27th Thekkady, Hotel: Taj Garden Retreat
Dec 28th drove to Madurai, Hotel: GRT Regency (good!)
Dec 29th Madurai, Hotel: GRT Regency
Dec 30th drove to Tanjore via Trichy, Hotel: Sangam
Dec 31st Tanjore, Hotel: Sangam
Jan 1st drove to Pondicherry, Hotel: Anandha Inn
Jan 2nd drove to Mamallapuram, Hotel: Mamalla Heritage
Jan 3rd drove to Chennai, Hotel: GRT Grand
Jan 4th flew 9W to Port Blair, Hotel: Fortune Resort Bay Island
Jan 5th ferry to Havelock, Hotel: Barefoot Resort
Jan 6th Havelock, Hotel: Barefoot Resort
Jan 7th Havelock, Hotel: Barefoot Resort
Jan 8th ferry to Port Blair, Hotel: Fortune Resort Bay Island
Jan 9th flew 9W to Delhi via Chennai, Hotel: Radisson Delhi

The Andamans were definitely worthwhile trip. Havelock island was great, very laid back and some of the best scuba diving I've done. We flew Jet Airways from Chennai ($325 R/T), their service onboard was excellent. The Barefoot Resort at Havelock was a good place to stay, it was remote and a long way (12km) from the main town/jetty. A long way from anywhere really. A 2 hr flight from Chennai, followed by a 2 hr ferry ride and a 20 minute ride in a tuk-tuk is about as far away as you can get! The beach (No 7) was voted the best beach in Asia a few years ago, and I can vouch for that. Super soft white sand, clear water and snorkeling right off the beach backed by a jungle.