1 month Indonesia, 1 month Malaysia

I don't know if the whole home base thing wouldn't work great - but here's some places to start researching:

Kuching, Sarawak - my favourite city - note in Borneo you will end up flying between cities.
Brunei is not Malaysia but if you go to Borneo definitely go there
Lake Toba in Sumatra I have a soft spot for - but you'd need to research current conditions.
I personally can't stand Bali - but that probably just me - its too Western - avoid totally if its school holidays in any Australian state
KL is a great city - as is Singapore - again not technically the countries you asked about - but you'll pass through.
Note Malaysia- particularly I expect will be slow in reopening to visitors - plus Sabah and Sarawak set their own rules for entry

We traveled through Malaysia for a month last February March just before the pandemic. We came by ferry from the Thailand islands so we started with a week in Langkawi. Good beaches. Then 2 weeks in Penang. Good food, culture, history. By train and taxi we visited Taiping, Ipoh, and Mallaca 4-5 days each. Small cities with beautiful parks and historic places. Ipoh has spectacular buddhist cave temples. I would recommend all of these places. At least read about them in your guide books and see if they excite you. We planned to finish with a week in Kuala Lumpur but left early, managing to get a flight to Honolulu two days before Malaysia completely shut down all transportation. Hope it’s open for you next year.

Lonely Planet has a new Indonesia guidebook coming out in Oct. I would buy that to help narrow down the top sights you don’t want to miss. Their new Kuala Lumpur & Melaka book won’t be out until Jun ’22, so you may want to buy the 3rd edition that’s available now.

I have been to both countries, as well as Thailand, Singapore and the Philippines.

Singapore is not to be missed. I recommend spending 4-5 days there. We like Malaysia more than Indonesia. Bali, was beautiful, but we have a negative view of Indonesia from the start when our cruise ship had to wait 2.5 hours because the cruise line didn't bribe the local authorities enough and more negotiations ensued, with everyone waiting to disembark.

Malaysia seemed more economically advanced than Indonesia. Singapore is first world and very modern.

The Philippines is far more Americanized and everyone speaks English, I would recommend it.

I am also planning a future trip to SE Asia. Sinc my wife has not been to that part of the world I'm planning to start in Singapore and move from there to Penang.
KL has never been a favorite so we'll skip past there. The coast is far more interesting.
We'll head from Penang to Thailand and then Cambodia, Laos and Vietnam. I'm hoping to time the trip to hit the peak durian season...I'm super stoked to get into some Red Prawn, my wife, not interested at all. I'll need to count on my local buddies to share it with me.
One thing to consider. The vacination rates there are far behind where we are. A friend in Penang told me they just started getting vacinations a few weeks ago.

Just a cautionary note that Jan/Feb will be in the middle of the annual monsoon. Not that big a deal in Malaysia, Thailand or Singapore but as I recall it's particularly wet in Indonesia ... am thinking in particular of Jakarta and Bali.
We lved in Singapore for several years and I have to opine that a full month in either Malaysia or Indonesia would be massive overkill. Unless your hearts are absolutely set I suggest looking further afield to perhaps include some of the other options in the region. Singapore is terrific, as are Hong Kong ... to include Macau and maybe a quick day trip across the border to Shenzhen in mainland China, and perhaps Thailand and Viet Nam if you've not already been to either. .
The SE Asian countries have their own versions of low cost airlines that will get you where you want to go cheaply and efficiently.

I had a 3 week trip to Malaysia years ago, but it wasn’t January/February. The east and west coasts have different wet and dry seasons - my trip focused on the less developed east coast for this reason.

We started with 5 nights in Singapore - we should have added a couple of nights extra including getting over jet lag. Moving from the highly developed, very western Singapore to the much more sedate Malaysia was a complete culture shock. We swapped traffic noise for the sounds of the mosques calling within a couple of miles.

We took a bus across the straits and picked up our hire car in Johor Bahru and headed up the east coast. We hadn’t booked accommodation for this part of our trip, but we took recommendations from Lonely Planet. We had a few nights further up the coast on Redang island then headed to Taman Negara national park for some wildlife spotting in the rain forest and boat trips on the river. After retrieving our car, we went to the Cameron Highlands, the tea plantation area, which was much colder, being at altitude. Our car only had A/C, not heating so we had to pile several layers of clothes on to keep warm.

We had a few nights in KL before returning to Singapore.

I can’t recall meeting many locals - in rural parts, many didn’t speak English.

Indonesia has developed significantly since I was there about 20 years ago. The islands vary significantly, so I suggest that you need to check out a guide book to establish which would suit best. I covered Bali, Lombok and eastern Java. Lombok was far less developed than Bali at the time, but even today, if you focus further north, you can avoid the party hotspot around Kuta and Sanur. The mountains and paddy fields are worth visiting.

Java freaked me out as the locals kept coming up to me and stroking my hair as it wasn’t black like theirs - this may have changed these days. There are some interesting sights such as the temple at Borobudur, but you need to visit early as it’s very hot there. Nothing was possible between about 10am and 4pm due to the heat.