Borneo is the absolute best. For above water activities the Kinabatangan River is an absolute MUST. Not overpacked with tourists because of its location but absolutely worth the trip. I spent 8 months in Borneo and this is the one thing that I couldn't recommend more. Proboscis Monkeys, Orangutans, Pygmy Elephants, Crocodiles, exotic birds, and much more.
As far as diving you have a lot more options than what people think. Sipidan is the obvious choice and well worth the money in my opinion. You have 2 options for areas to stay. One is the city of Semporna which is the less desirable of the 2. Honestly I only passed through Semporna because I had heard it wasn't a place I needed to see unless I was staying there to take the boat to Sipadan. The 2nd option is the two small islands close by Sipadan, Mabul and Kapalai. They make for closer boat trips to Sipadan and nice resort accomodation. There are two main resorts that divers stay at, Scuba Junkies and Borneo Divers. I stayed at Borneo Divers which I believe is just a slightly more expensive option. But everyone I talked to at Scuba Junkies seemed to be enjoying it. Borneo Divers had everything you'd expect from a dive resort and I would book again. Budget is the main factor in your decisionof whether to stay on the islands or in Semporna. Unless you just really want to try and sight see Semporna but I don't think thats what most people do. Its worth mentioning that Sipadan is amazing but I'm more of a macro lover. I actually found myself just as excited to dive the artificial reef at the Kapalai Island. It is easily the best macro dive I've ever done. Multiple Ornate Ghost Pipefish, multicolored frog fish, and countless nudibranch. The Mabul and Kapalai dives aren't as picture perfect, but if you go into them knowing its for the macro and not the schooling fish and coral like at Sipadan, to me they were just as good.
Also, if you find yourself in Kota Kinabalu I would highly recommend Palau Tiga (Survivor Island) if you like macro diving. I'm not really sure how to get there because I was fortunate enough to be on a private boat, but I was told there are charters from KK you can hire. I'm going off of my memory for all this, so I may be slightly off on some of the details, but I remember this one incredible macro dive. It was a few miles away from Palau Tiga if I remember correctly. The site was around some permanent metal structure sticking out of the water, maybe that will help you find it. It wasn't easy logistically to get there but man was it worth it. I don't think it ever gets dived there wasn't a single other dive boat the few days I was at Palau Tiga. Again it wasn't a stunning coral/schooling fish dive. But such incredible macro if you're into that kind of thing. Anyway I hope you get something out of this and enjoy Borneo as much as I did. I'll definitely be back.