I am planning on taking an 11-12 day trip to Southeast Asia. I am pretty set on Thailand, but I am also thinking of going to Malaysia or Indonesia for part of the trip. I am interested in the more exotic and natural things to see like beaches, rain forests, elephants, ancient temples in the jungle, etc. I am thinking that I will most likely fly to Bangkok and then take a flight on an Asian airway to get to somewhere like Phuket or Krabi, then possilbly Kuala Lumpur or another place in Malaysia. Any recommendations would be helpful!!!

Of course the king of ancient temples is Cambodia, but you can also see plenty of ancient sites in Thailand which also has many large national parks with plenty of nature to see. And of course there are several elephant experience places in Thailand as well. With that many (few) days I would consider just staying in Thailand. Maybe head up to Sukhothai for the old temple sites there. And there are big national parks nearby that area too with interest rock formations and plenty of jungle/forest. Or head east to Isaan. Maybe visit Phimai and Phnom Rung for the old temples. There's the massive Khao Yai national park near Khorat with waterfalls, meadows, forest, etc. Chiang Mai and Chiang Rai and that whole northern part of the country also has great parks and mountains plus some elephant camps.

I suppose time of year might make a slight difference as well.

Yogyakarta has a very nice temple in it. The non-touristy areas of Bali are quite nice, too. So, if you decide on an Indonesia side trip, those are quite nice. Sumatra also has some Orangutans, and I'm sure Borneo has some, too.

If you just want to interact with animals, there is a Taman Safari animal park outside of Jakarta. You drive through the park, and then they have an animal center where you can hold some of the animals, get pictures taken for a small fee.

Air Asia has some cheap flights within Asia. 2-3 times a year, you can get flights almost free. Sign up for their emails, or Facebook page, to get advance notice of the sales.

Note: Air Asia charges you for almost everything. So if you want to check luggage, choose a seat, or bring food, it's going to cost you. Generally, I don't recommend paying for seats until the week before the flight. That way if you're not going to fly, you don't lose that money, either. I only pay for seats ($2 or so), if I think the flight is going to be full.

Thailand: the old capitol Ayutthaya; about 90 minute drive from Bkk proper

Indonesia: Borobodur in central java, need to fly from Jkt to Jyojakarta.

Cambodia: Angkor Wat in Siem Reap, plan on 2 days.

Agree with the Angkor Wat/Siem Reap (Cambodia) recommendations, but I would devote four days.

My personal favorite is always Northern Thailand. I like Mae Hong Song and Nan especialy well.
Laid back and not too many tourists.
Menko

http://www.asian-oasis.com/product/mekhala-cruise/

There's nothing really "exotic" about most Thailand beaches. Lots of tourists. Thailand (Bangkok-Chiang Mai) plus 2-3 days at Angkor would be a great first-time trip!