Start from pune in the evening. You can take sleeper class bus. you will reach Panaji ( capital of goa ) early morning. Book cab and go directly to south goa. Most popular beach is Paloem beach. On first day in south goa you can enjoy paloem beach, please do kayaking and go to honeymoon and butterfly beach. In evening enjoy sunset and if you are interested you can go to silent noise disco. It will be really amazing experience. Next day cover old goa, mangeshi temple, baga beach, calungut beach and casino. on last day after check out come to panaji you can do some shopping here and can catch a bus to Pune.
Having stayed in Goa for the past 3 years, I would suggest you that the best would be that you stay anywhere in South Goa, as this place is a very quiet and pleasant area with not much crowd and amazing things to do.
For the weekend I would say, the first day explore the localities of South Goa, check out the restaurants there and as the day ends stroll on the beachside during sunset holding your wife's hand and enjoying the slight breeze taking all your tensions away and giving you the ultimate bliss in life... Sit along the beach for a few hours and let your body melt into the surroundings and relax. The next day, if you would like to explore you can rent a scooty and explore the whole of North Goa in a day. If you are interested in water sports do visit the vagator beach which is generally crowded. Also, you could visit aguada fort, Candolim beach and chill-out at a disco in the night. This would be a nice weekend together for you and your wife just like a mini honeymoon.