Quite hectic if I may say First of all lonavala/khandala and matheran are monsoon destinations. Any other season you won't enjoy. I would suggest a day or two in pune covering dagdu sheth ganpati, shanivar wada, a few temples in old pune. And then cover bhimashamkar and other stuff
Please do keep in mind that Matheran would involve a lot of walking since vehicles are not allowed in Matheran. All vehicles are parked at Dasturi Naka and from there on only horses, hand pulled rickshaw or walking is the option to see the different points which are spread all over Matheran.
Lonavala / Khandala do not have a lot of options for sight seeing. There is a wax museum, Narayani Dham, Bushi Dam, Valvan Dam etc. If you are interested in para gliding Kamshet could be an option.
In Pune there is a sight seeing bus organised by the MTDC or the municipal corporation which takes you to around 10 sights in Pune. See http://pmpml.org/pune-darshan/
Pune is for serious people, nothing in Pune can be passed off as timepass!! :rolleyes:
Anyways - a good option then is to take the Pune Darshan bus - covers many of the important points in Pune and you have a guide to help you understand the importance of the places. Details of places covered here.
If this suits you, then on day 2 you could cover - Sinhagad fort, Parvati, do an actual visit to Vishram Baug wada, pay your respects to Dagduseth Ganpati, visit Lal Mahal and finish it off with light and sound show at Shaniwarwada in the evening.
If you want to go away from the city a visit to Lavasa could be an option (not recommended as day visit - nothing much to 'see' there). An excursion to Tikona fort with Hadshi temple enroute for the adventure minded.
Note - Please do not take snotty too seriously except in serious matters!
Do rethink about Lonavala/Khandala as RD mentions - too much of concrete and traffic and less of nature now over there! (unless you have booked your hotels there and then we will tell you how fantastic these twin towns can be and places you would love to visit when you are there!)
Do go with snotty's advice. Trust me many of my relatives forced me to take them to lonavala and khandala in December and January and came back disappointed. For an excursion you can go to lavasa or bhimashamkar. And to add to the list do visit the Ram temple at tulsibaug. Its a hidden jewel. An oasis among the chaos
The worse thing that happens is when you have finalized your plans and others are giving you advice to the contrary. All we are saying is that it is usually way better in monsoon, but since you are not coming in monsoon - do go ahead and visit as planned.
As for Pune - for day 1 - you can plan the city - visit Dagduseth Ganpati, go to Tulsibag for some women shopping (it is amazing how time passes without your realisation), Ram Mandir as RD says for some peace (especially for male companions while the women are shopping), Vishrambaug Wada, Lal Mahal and finish with the light and sound show in Shaniwar Wada. If you love spicy stuff - there is bedekar misal in Tulsibag or if the sweet tooth rules - Kawre cold drinks in the same place could interest you.
Day 2 - I will leave this for some else to plan! ;)