So just to clarify before I start - this post is a comparison of the value for money and effort on Kilimanjaro vs Kinabalu. You can’t really compare mountains as they are all very different. The best answer in general is to climb every mountain you can, and them some more!
Also for background, I did Kili in 2015 and Kinabalu in 2018. My hike report for Kili is somewhere online, although seemingly not on my blog. When it is posted there, I will copy the link here as well.
My writeup on Kinabalu is at:
I am going to compare the mountains from a few different points of view. I did Kili through Zara Tours, organised by Summit Ventures on this side, flights on Air Kenya. I did Kinabalu through Amazing Borneo (the only operator on the mountain) and flew Air Mauritius.
Some background on the mountains first:
Kilimanjaro (or Kili for short) is the highest mountain in Africa, 4th most prominent mountain on earth and 4th most isolated mountain on earth. It has a few glaciers left, although they are sadly melting very quickly. The mountain rises above the town of Moshi to an altitude of 5895m and is absolutely massive. It is flanked by Mawenzi to the east and Shira to the west. Meru is also clearly visible from it.
Mount Kinabalu is the highest mountain on the island of Borneo, the highest point in Malaysia, 20th most prominent mountain on earth and 19th most isolated. The summit is 4095m, and it is only 38km from the sea - meaning that you can actually see the sea from the top. Trus Madi is the nearest high mountain, but it mostly stands alone above the city of Kota Kinabalu.
Visa requirements
At the time of travel, neither country required a via. To the best of my knowledge, this is true of both at the time of writing, but these things can change, so best to check before you book.
Travel time
The cheapest flight when I did Kili was through Nairobi. So a 6 hour flight from JHB to Nairobi, about a 3 hour delay before a 1 hour flight to Kilimanjaro International Airport.
Malaysia is much further away. I flew through Mauritius and Singapore, but a brief google search tells me the cheapest option is to fly JHB - Mauritius - Kuala Lumpur (KL) - Kota Kinabalu (KK). Air Mauritius to KL and Air Asia or Malaysia Airlines to KK. So that is an extra flight, and unlike Air Kenya, the leg to KL or Singapore is not done daily, so you might have a stop over for a night in Mauritius (aka a cheap short beach holiday 
).
The drive time from Kili Airport to Moshi is about an hour, and then you have another hour to the start of most of the routes. Transit to Mount Kinabalu is similar.
Convenience
When I arrived in Tanzania, a driver had a sign with my name on it and drove me to Moshi. The next day, we were driven to the mountain. This was all part of the package. After the hike, transport back to Moshi, and to the airport the next day was also included.
When I arrived in KK, we caught a taxi to our accommodation. If you have the Grab app set up on your phone beforehand, this is even cheaper (about R35 from the airport to the city centre). Petrol in Malaysia is very cheap. We sorted out our own accommodation in KK. We stayed at Borneo Backpackers, which cost about R150 pppn for our own private room with 2 people in it, and included an air conditioner (all the rooms have this). On the morning of the hike, we were picked up from Borneo Backpackers and taken to the mountain and after the hike we were dropped back at Borneo Backpackers.
Neither accommodation was particularly amazing, although Borneo Backpackers was nicer than the place in Moshi - mostly because it included an air conditioner. Moshi included meals, Borneo Backpackers “includes breakfast”, but that is just toast and coffee.
It is notable that Borneo Backpackers is within easy walking distance of over 20 restaurants, and if you are eating local (i.e. not pizza or burgers), you can get a large plate of really good food for about R25. Luckily I quite like chicken and pasta!
So slightly more planning is required for Kinabalu, but both hold up very well on this one.
Guides
Our guide on Kili was a man named Dickson. He is a veteran of over 20 years on the mountain, and was incredibly knowledgeable about local history and did an amazing job.
Clarence on Kinabalu disappeared right near the start, we barely saw him over the length of the hike, he told us very little baring where to be and when. I don’t know if this is normally how it is done, but really our guide felt more like a formality than part of the experience.
Both sorted out our paperwork for us.
Duration
I did Machame route on Kili over 7 days. So it was 9 days between leaving home and returning.
Kinabalu is a 2 day hike, or 3 day if you do the Via Ferrata.
So Kili can be done as a standalone trip, but when you start adding other parts, it becomes a fairly long time to get off work.
Kinabalu takes a while to reach due to it being double the distance away. The hike itself is only 2 days, so not worth going all that way just for the mountain. But Tunku Abdul Rahman National Park (5 small islands off the coast of KK) makes for a great, and surprisingly cheap, day out. There are also lots of places nearby for game viewing, or you can head out to Mulu, Kuching, Sandakan etc to see caves, turtles, orangutans or whatever you want to do (or you can chill on the beach on one of the islands). Internal flights on the island are super cheap - I got my flight to Mulu for R400 each one way due to a special.
So basically Kili can be done as part of a longer trip or in isolation. Kinabalu needs to be combined with something else.
Food
Both mountains included food as part of the package.
Food on Kili was porridge for breakfast, a packed lunch (usually full of fried carbs) and supper was some fruit/peanuts/popcorn, soup (cucumber soup was amazing), some form of fried meat and some fried food with it. Sometimes with rice or pasta. I can’t say I particularly enjoyed the food, but it served the purpose.
Kinabalu starts with a packed lunch. This was some sandwiches, fried chicken, and egg and an apple. Aside from the packed lunch, though, Kinabalu beats Kili in the area of food. Included in the package is supper at Panalaban Hut, breakfast before summit, breakfast again after the summit and lunch at the end of the hike. These meals were all buffet and the food quality was very good. I will continue my search until I find someone who makes black pepper lamb like that again!
Quantities of food on both were more than enough.
Comfort
Kili is generally done with tents. Coca Cola Route has small huts, but I hear these aren’t nice. So Kili does have the more authentic feel.
Kinabalu has Panalaban Hut - which includes bedding, hot water showers and even food for sale.
So Kinabalu is definitely the more comfortable option. It is also only 1 night vs at least 4 on Kili - so if you are looking for a more comfortable option, Kinabalu is it. I personally give Kili the points on this question simply because a tent feels far more authentic than a large hut at 3275m!
Porters
Kili includes compulsory porters. This boosts the local economy via job creation. Conversely it means that a lot of underpaid workers who work a week or 2 a month have to do backbreaking work all day. So you can argue this one both ways.
Kinabalu also uses porters, but they are carrying supplies up to the hut. Because they do it round trip in a day, they don’t have to carry their own gear. They also aren’t carrying your items. You can hire a porter on Kinabalu, but I have no clue what you would give them, you basically have nothing in your pack to start with.
Ablutions
Neither mountain allows you to “go” in the bushes. Kinabalu has more frequent toilets, though. Although both could use one closer to the summit.
On Kili you wash off in a bowl of warm water. Kinabalu has hot showers.
Scenery
Lower down, both mountains are rainforrest - so actually very similar. Naturally they are different types of plants, but to a non-biologist, both look very similar.
Around 4300m, Kilimanjaro becomes Alpine Desert. This is really beautiful in a haunting kind of a way - if that makes any sense. It is very stark and inhospitable. It looks like a place where you would find skeletons - but nothing lives up there, so nothing dies up there. It is not pretty.
Kinabalu goes directly from beautiful green vegetation to rock. The summit is very spiky and featured. It is definitely a much prettier mountain.
From Moshi to the summit of Kili is about 5km in altitude. KK to the top of Kinabalu is about 4km (KK is at sea level), so Kili is bigger. Kinabalu is much steeper, though. This means it is a much more dramatic peak.
The view from the top of Kili isn’t particularly amazing. The glaciers are awesome, and Meru is there in the distance. But pollution was bad when I was there (hard to tell if I was unlucky or this is normal).
From the top of Kinabalu you can see the city below, the sea in the distance, and all the spires of the summit around you. There is also the view down the infamous northern gully, which is really something.
To be honest - Kinabalu beats Kili on this one. Incidentally, the Drakensberg beats both of them (but I am biased on that one).
Difficulty
Both are hikes. Both have very light scrambling and very good trails. Kili summit day is longer than the entirely of Kinabalu and overall is more than 3 times the distance. Kili also has more altitude, which makes a huge difference.
That being said - relatively speaking both are easy as far as big mountains go.
Cost
I did Kili when the Rand was R9.50 to the USD and Kinabalu at R14.70 to the USD. If you account for the USD cost of the trips, my entire 4 week trip to 3 countries cost about the same as my 9 day trip to Kili. Notably Kinabalu was the most expensive part of that trip (aside from flights). So the all in cost of just Kinabalu about half of Kili.
Overall
I feel the only reason to do Kili is because of sentimentality. The ascent is massively overpriced, and very little of that money is going to good causes such as conservation and sustainable development. Tips given to tour organisers for the porters often don’t even end up being given to the porters. There are closer similarly impressive mountain trips one can do - such as a visit to Reunion Island, or even the Drakensberg.
I make the comparison to Kinabalu simply because nothing nearby can compete in terms of scale. Notably you can hike to Everest Base Camp or a number of Andes routes for a fraction of the price of Kili - but I haven’t done these, so I can’t make an appropriate comparison.
I climbed Kili for personal reasons - it was something I had wanted to do since I was little. A year ago I didn’t know Kinabalu existed. If I had to do one again, it would naturally be Kinabalu - but I would rather take on any number of large mountains globally ahead of either.