The big question EVERYONE is hoping for...what is the best route to explore Southeast Asia?
Well, there is no actual right or wrong answer, but there are routes to minimise going back on yourself and the amount of money spent.
To find out what we have concluded as the best route, you need some extra information:
The planned route
The actual route
The best time to travel
The planned route

Before travelling anywhere, we did some research and found that the places we were hoping to visit, fell under what is one of the most well-known routes for backpackers in Southeast Asia. This route is known as the 'banana pancake trail'.
The route originally consisted of Thailand, Laos, Vietnam and Cambodia, but has since been stretched to countries such as Malaysia, Indonesia, Philippines, Myanmar, Sri Lanka, India and Nepal. The reason for this extension is the influx of travellers, the popularity of travelling and more travellers dedicating an extended amount of time to travel.
Side note - it is named the 'banana pancake trail' as each destination serves banana pancakes as a sweet treat and not because the four countries look like a banana and a pancake.
This route is also incredibly popular for backpackers due to its ease of travelling from country to country as well as its cheap offerings such as food, accommodation and activities.
So, the plan...

The plan was to start in Thailand, then travel by train or bus into Laos, Vietnam and Cambodia, and then from here we would fly to Malaysia, Indonesia and the Philippines.
But, as people always say, plans never go as planned!
The actual route
Thailand
Bangkok > Chiang Mai > Koh Samui > Koh Phanghan > Koh Tao > Khao Sok National Park
Bad choice in time to go to the Koh Islands because we got stuck in lots of rain.
Laos
Vientiane > Thakhek > Vang Vieng > Luang Prabang
You have an option to travel to Vientiane from Bangkok on a long 25 hour bus or a short one hour flight. It was a no brainer, but obviously a bit more expensive.
Vietnam
Hanoi > Ha Giang
Bad choice in visa meaning we had to leave the country and enter rather than continue down the country as planned.
Malaysia
Kuala Lumpur > Georgetown, Penang > Kota Kinabalu > Sandakan > Semporna > Tawau > Melaka
Bad choice in time to go to Borneo because we got stuck in even more rain.
Indonesia
Ubud > Canggu > Sideman > Nusa Penida > Gili Air > Senaru > Tetebatu > Kuta
Bad choice in order as we had to travel passed Ubud to get to Sideman from Canggu.
Cambodia
Phnom Penh > Siem Reap
Vietnam
Ho Chi Minh City > Da Lat > Hoi An > Da Nang > Hue > Hanoi
Laos
Luang Prabang > Nong Kwiaw > Vientiane
Overall this route was pretty good with some weather issues. Our biggest problem was having to move out of Vietnam and then entering later on. If it wasn't for having to do this, I probably would have suggested this route.
So note to self - take the 30 day visa, always!
The best time to travel
Thailand
Chiang Mai - Nov to Dec - Nice heat and avoids burning season
Bangkok - Nov to Dec - Cooler weather
Koh Islands - Dec to March - Settled weather
Yala - Dec to Feb - Small rainfall and cooler temperatures
THAILAND = DECEMBER
Laos
Vientiane - Nov to Feb - Sunny days and comfortable weather
Luang Prabang - Nov to March - Dry and comfortable
Pakse - Nov to March - Dry
LAOS = DECEMBER/JANUARY
Cambodia
Phnom Penh - Nov - April - Sunny and dry weather
CAMBODIA = DECEMBER/JANUARY
Vietnam
Hanoi - Nov to April - Low rainfall and sunshine
Hoi An - Feb to April - Warm weather and little rain
Ho Chi Minh - Dec to March - Settled weather
VIETNAM = FEBRUARY/MARCH
Malaysia
Kuala Lumpur - May to Sep - Remains relatively dry
Singapore - February to April - Least amount of rain and low humidity
Sabah - May to Sep - Dry season
Sarawak - April to Sep - Drier in weather
MALAYSIA = APRIL/MAY
Indonesia
West Samatra - May to Oct - Dry season
Java - May to Sep - Hot, dry and sunny
Bali - May to Sep - Settled weather
Lombok - June to Sep - Less rainfall
East Tenggara - July to Aug - Plenty of sunshine and dry
INDONESIA = JUNE/JULY
All are pretty hot all year round. From our experience Laos and North Vietnam are significantly cooler Mid-Dec to Mid-Jan.
So the main event…
The best route
Starting in December, fly to Bangkok.
From here, move down to the Koh Islands (Koh Samui, Koh Phangan and Koh Tao) via Surat Thani by bus and boat. Then, journey back up the country to Chiang Mai via Bangkok by boat and bus. Heading to Chiang Mai last will allow for easier access to Laos.

Moving from Chiang Mai, make your way to Luang Prabang.
This may be a 21-hour bus or a 1-hour flight. Obviously, the flight would be more expensive but it will save you a hell of a lot of time.Next, head up to Nong Kwiaw and back down passed Luang Prabang stopping at Vang Vieng, Vientiane, Rock Lodge/Thakhek, Pakse and Don Det (4000 Islands).

From Don Det, get an 8-and-a-half-hour bus to Siem Reap, and then onto Phnom Penh.

Cross into Vietnam, starting in Ho Chi Minh City, and travelling up the rest of the country.
Stopping at Da Lat, Hoi An, Da Nang, Hue, Hanoi and Hi Giang. All achievable by bus.

The plan from here is to fly to Kuala Lumpur, Malaysia.
From Kuala Lumpur, travel up to Georgetown, Penang to travel back down passing Kuala Lumpur to Melaka.

Now you want to head to the jungle side of Malaysia, Borneo.
Fly into Kota Kinabalu and grab a bus to Sandakan to visit the Kinabatangan River. Continue around the coast, stopping at Semporna and flying back to Kuala Lumpur via Tawau to travel to Indonesia.

Fly into mainland Indonesia, starting in Jakarta and moving to Yogyakarta. Continue across the country and grab a 4-hour bus to Bali via Banyuwangi and then a 1-and-a-half-hour speedboat to Lombok.

In Bali, we suggest visiting Canggu, Ubud and Sidemen. While in Lombok, we suggest visiting Seraru, Tetebatu and Kuta.
Despite this being my personal suggestion, I am sure there are hundreds of ways to do it.
Overall, considering the time of travel, events, activities and locations will be the biggest factor in determining your plan. And if things do not go as planned, well, that is all part of travelling.
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