3 Month SE Asia and Korea Trip

Firstly, let me say this sounds like a fun and well thought out trip. On Thailand, I think your main issue is it's not a great time to visit Chiang Mai and the North, as you have correctly observed, it is burning season. But having lived there, I have to say it's my favourite part of the country. So a bit of a dilemma, because it's an amazing region and seems to fit well with your interests.

On Indonesia, I would recommend Yogyakarta when you're in Java, as a really interesting historical city. I'm not really a fan of Bali, as it can be very, very touristy (albeit you can travel out of the south). You could spend all that time in Java.

I'd be inclined to add Malaysia - either Penang (amazing historical architecture) or east Malaysia, perhaps Sabah (if you really want to see jungle, nature, wildlife etc).

I say post your question in tripadvisor Thailand and Indonesia, you will get tons of great responses from them.
I did when i planned my trip to Bali and Yogyakarta.
You can also go to Lombok, Flores, trip to Komodo island/national park, do liveaboard boat trip from Flores, Mt Bromo, Ijen, etc. Lots of places to visit. 19 days may not be enough 😀

Suggest that you research and consider historical weather patterns in Asia before you finalize your itinerary.
Korea for example tends to be cold and gloomy in January but things will improve dramatically the closer to Spring you visit, ie March would be better.
As I recall Jan-March tends to be the winter monsoon season in Indonesia, while other destinations in SE Asia (Singapore, Thailand, Laos, Vietnam, etc) tend to be a little drier and a bit more temperate.
Point being that if you time things wrong you could be in for major disappointment ... or at least a very wet and soggy trip.

Scuba diving you say? This would appear to be the unaddressed elephant in the room. I assume you are already certified? What's your experience level?

You are headed to some of the absolute best diving locations in the world, including many that really make everywhere else pale by comparison (I've dived in a lot of the world; the diving I've done in Indonesia was so much better than than anywhere else I've ever been - it's like a whole 'nother planet).

If you are a diver, it would be a crime to not put a serious focus on that as part of this trip. Yes, it'll take time away from other places and things, but if you don't include some diving you will kick yourself later for having skipped the best diving (by far) in the world.

I have a Padi openwater certification. I'm definitely still a beginner though. On top of the certification I've done a few dives in Colombia, Brazil and the DR, really enjoyed it but I wouldn't consider myself a diver and wouldn't specifically design my trip entirely around diving.

Because of Ramadan and the monsoon season I'm starting to think it might be best leaving Indonesia for another trip. Are there any spots maybe in Thailand, Malaysia, Cambodia or Vietnam that you would specifically recommend for diving?

I have a Padi openwater certification. I'm definitely still a beginner though...

Good news: your basic PADI OW cert (and a modicum of buoyancy control) is all you need for what would be incredible, spectacular (some might even say, life-changing) diving in Indonesia.

I've done a few dives in Colombia, Brazil and the DR...

With all due respect, while those places are great destinations – as the expression goes, "any day diving is a good day" – there's no great diving in any of those places (at least none that's readily accessible to a casual tourist and an inexperienced diver - Colombia has some epic world-class dive sites but they are extremely remote and require National-Geographic-level live-aboard expeditions and $$$$ to get there; I suspect the same may be true of Brazil; the DR is a nice easy fun-in-the-sun location but not known for quality diving, and pretty much all of the Caribbean marine ecosystem has suffered tremendous damage...most of the Caribbean's reefs are dead or getting there).

OTOH, Indonesia has by far the most spectacular diving in the world, and a lot of it is relatively easy to access. It is a diver's paradise. You have never seen anything close to a healthy, vibrant, coral reef. There's probably no place better on this planet than Indonesia to experience life underwater for even a casual diver. Get out a map and take a look: Indonesia is a huge country, it consists of thousands of islands, and it sits smack dab where the tropical Pacific and Indian Oceans meet and mix: it is the ecologically richest, most biodiverse stretch of the entire planet (aka "the Coral Triangle"). It's like no place else – literally. The underwater environment is still pristine and thriving, and it doesn't require a great effort to get out to extremely remote places to find spectacular, vibrant reefs that are still absolutely overflowing with life. It also happens to be a wonderful destination topside, with all the things (and more) that one dreams about for tropical destinations.

I wouldn't consider myself a diver and wouldn't specifically design my trip entirely around diving...

You have already gone through all the time, trouble, money, and effort to get your SCUBA certification - not a trivial accomplishment (and the primary barrier that prevents 99.9% of others from experiencing most of the places on this planet). How did that happen if you have little or no desire to experience diving?

Let's assume you're not particularly religious. If you were going to France, would you skip Chartres Cathedral or Notre Dame? If you're not a big art enthusiast, would you bypass Michelangelo's David or the Sistine Chapel on a trip to Italy?

The living reefs of the Coral Triangle are mother nature's Sistine Chapel and Chartres Cathedral. You're going to be Right There. You have everything you need to go experience these magical wonders, all you need to do is go look. You have an incredible opportunity here to experience some of the world's greatest treasures, one that many would jump at (and one that many people would indeed gladly build a trip around). Your trip, your choice. But to me, what a tragedy it would be to waste this opportunity.

I hope this gives you something to think about.

PS: Don't touch the reefs (that kills them).

Sounds like an amazing trip. I will be in Taipei, Siem Reap, and North Vietnam in late February, early March.

As for Sapa, I was also considering it but ruled it out. I have less time than you, which is a factor, but I also ruled it out due to time of year. February is not supposed to be a great time to go, due to weather, and because the views are much prettier when the rice paddies are golden. As it is a bit of an outlier, and my trip is only for 3-weeks total, I decided against it. You have a much longer trip (but also more places on your itinerary), but unless you go in the latter part of your trip, it may not be worth the extra time it would take.

Of course, I haven't been there, so perhaps someone who has would have better insight than I do.

Anyway, have a wonderful trip.

"Because of Ramadan and the monsoon season I'm starting to think it might be best leaving Indonesia for another trip. "

I think you're overthinking this - I wouldn't avoid Indonesia just because of Ramadan (it is a majority Muslim but multi-religious country so if you're worrying about getting a meal during the day, don't), and also, remember that Malaysia is also a majority Muslim country, so many people will also be observing Ramadan.

In terms of seasons, the rainy season will impact Malaysia's east coast at this time.

We were in VIetnam late March, into April- 22 days and did not get to nearly as many destinations as you have listed. HaLong Bay was a disappointment as was Phu Quoc and we didn't get to Sapa- too far. We loved Hoi An, Hanoi, Hue, Nin Binh/Tam Coc and Phong Nha- it was definitely a highlight. Travel between places is slow. We booked several internal flights to save time and when booked early they were inexpensive. If you like adventure activities you really should look at Phong Nha, we stayed 5 nights and could have stayed longer. Our time in Vietnam was part of a 7 week trip, we were also in Thailand but due to timing of the burning season also skipped Chiang Mai- we will definitely be going back Thailand and Cambodia.

I may be in a minority, but I really, really didn't love Sapa. We were there in March and the rice fields, while gorgeous, were big ole' mud pits when we hiked through them. We were literally just slipping and sliding around them. Our guesthouse set us up with Hmong guides for this and while lovely, I have never experienced such a hard sell in my life. It was constant the entire time we were there. And if you bought anything, it just increased demand to buy more. They make the carpet sellers in Istanbul look tame, no joke. My friend finally put them off by saying "Maybe tomorrow"; the next day, were were having a drink at a bar and the lady tracked him down.
Korea may well be extremely cold when you are there, so be aware of that. I'm not sure Jeju would be on my list that time of year because almost everything in Jeju is nature and outdoors.

A few things stand out - definitely consider extending your time in Indonesia based on what others said, even with the rain. And it's good you're rethinking Sapa since it does sound less appealing that time of year. Have you looked into Phong Nha yet? Seems like that could be a great alternative for your Vietnam plans. Happy travels!