Suggestions for 2 week itinerary?

With 2 weeks at your disposal I would warmly recommend to add part of Syria (Damascus) to your itinerary.

You don't have stated what kind of transport you're using. I would say work you're way down from Madaba (and the Bible sites near that) along the King's Highway to Petra. If you like nature don't forget to stop in the Dana Nature Reserve, where it's quiet and nice. Then you could go on (after visiting Petra and Wadi Rum) to Aqaba (for a dip in the sea) and work your way back through the Dead Sea Highway which brings you obviously to the Dead Sea.

I also miss Jerash (the old Roman City) in the north of Jordan.

And October is a good time of travel as the temperatures are not to high.

I made a 15 days trip in Jordan in last May , I loved it, the country is beautiful and has a lot to see and do. The itinerary for a trip in Jordan depends on what you like and you are willing to do.
Jordan also has fantastic natural sceneries and for those who like to hike and enjoy nature is a paradise.
My itinerary was as follows;
From first to fourth day I stayed at the Marian Hotel in Madaba and from there I visited:
Day 1: Madaba - St George's Church (the map), Archeological Park, Church of Apostle, Madaba Museum.
Day 2 - Full day tour to Pella, Umm Qais, Jerash and Ajloun Castle
Day 3 - Full day tour to Desert castles (Qasr Hraneh, Qusayr Amra, Azraq Castle) + Azraq Wetland Reserve and Reserve Shaumari Widlife
Day 4 - Full day tour to Iraq al-Amir, Salt, Fuheis and Amman (Cidatel, Roman Theater, and Souks Mosque)
On the fifth day I went to the Dead Sea, I stayed in Mujib Chalet in Wadi Mujib Nature Reserve .On the way from Madaba to Mujib I visited:
Day 5 - Mukawir (Herod Castle), Mount Nebo, Bethany (the baptism site) and went to Mujib where I spent the afternoon enjoying the wonderful Dead Sea.
Day 6 - I joined the Malaqi trail in Wadi Mujib Reserve
Day 7 - I spent the morning walking alone at fantastic Mujib Canyon and in the afternoon went to Dana. On the way to Dana visited Karak Castle. I stayed 2 nights in a hotel in Dana.
Day 8 - I went to a 6 hours hike with a guide in the Dana's mountains and explore the village and the surrounding area.
Day 9 - I did more a hike in the morning and in the afternoon I went to Wadi Musa. On the way I visited the Shobak castle.
Day 10, Day 11, Day 12 - I stayed in Wadi Musa visiting Petra, litle Petra and Wadi Araba
Day 13 - In the morning I went to Wadi Rum , did a full day tour on the desert and spent the night in a desert camp.
Day 14 - In the morning I went to Aqaba, visited the beaches and the city went to a boat trip.
Day 15 - I visited South Beach in the afternoon and returned to Amman ..... unfortunately my trip ended.
I think this itinerary is good and allowed me to see the Jordan's main attractions but if I could go back and change it I would change the following:

1 - I would be based in Aman and not in Madaba. Despite the city being pleasant I lost the opportunity to visit many places in Amman.
2 - I would be one more day in Wadi Musa and a plan a hike with a guide in Wadi Araba . Wadi Araba is fantastic.
3 - Add one day to take a tour to Disseh.

I agree with #2 and #3 that Dana should be included in your itinerary :)

Ahhh you are so so lucky to have 2 weeks! We spent a week in Jordan and then went to Damascus. Try to go there as you won"t regret it. Dana also a great idea in Jordan.

Vania - you seem to have covered a lot of ground!! How did you manage it? were you on an organised tour? How did you travel? I have 12 days in Jordan - travelling independently. Wondering how best to do it!! If you have any recommendations for guides or organisations please let me know! I am trying to do the trip on a budget!

Hello Mercedes
I traveled alone and independently. Organize a trip to Jordan is very easy, all you want to know you can find in Jordan Jubilee website (www.jordanjubilee.com).It is the most comprehensive guide for Jordan.
Despite what everyone say a trip to Jordan is relatively cheap, I'm trying to plan a trip to Syria and I am scared with the prices that are much more expensive than Jordan.
The most expensive on my trip were the tours that are arranged with hotels and travel from one city to another. A woman traveling alone can not take any taxi on the street and go to a place distant, spending more money for a driver provided by hotels is the price we pay for our security.
The first part of my trip the program until the arrival in the Dead Sea, I was using the organized trips of Hotel Marian.(http://www.mariamhotel.com). The other hotels, tours and all the programs I found asking informations for hotels and here on LP travel forum.
If you need tips and information to plan your trip I can help you.