I'm sure this response is too late for the OP but perhaps it could benefit on-lookers in the future.
I dove Cocos over last Christmas and was on one of the last Deep South Maldives LOBs before quarantine hit in March 2020.
Both are great destinations though both fell a bit short of my expectations. I wouldn't say the diving experience is at all comparable but I will try to highlight the experiences:
Cocos over Christmas: this is not the peak season in Cocos if you are going for the famous huge schools of hammerheads. My roommate on the boat was on her 10th trip to Cocos and recommends the North American summer season for that (June-September). I went last year over Christmas because CR was open and Sea Hunter were having exceptional sales. I can highly recommend the operation and crew (especially Manuel!). As I have dived Malpelo before, I didn't find Cocos diving conditions to be challenging at all though there are currents and negative entries (Manuel called it "Malpelo light"). There was one site where we descended one at a time on a line and the currents there were ripping (you really had to use your maximum arm muscles and kick hard to get down the line) but otherwise I found the dives pretty mellow. In December, I was comfortable in my 5 mm and hooded vest (and I run very very cold). The standard there is to descend to a cleaning station around 30 metres and find a somewhat comfortable place on a rock ledge so you can watch the sharks come by. Up-close encounters with hammers and Galapagos were common. We saw silkies and tigers along the reef/out in the blue a handful of times and even caught a juvenile whale shark on one dive. Our dive group ran into schooling hammerheads a handful of times but they tended to be a bit further out and didn't stay around us long. My experience end of August 2019 in Malpelo was waaaay better in terms of proximity and frequency of sightings of wildlife (e.g. schooling hammerheads on every dive, as shallow as 15 metres, oceanic mantas, tons of whale sharks, very busy cleaning stations with huge Galapagos sharks and lots of hammers, silkies and dolphines in the blue, free-swimming eels everywhere and a really interesting and diverse topography that included swim-throughs, walls, pinnacles, channels).
Deep South Maldives : I saw they are offering this routing in December and it surprised me as I had understood it was only really accessible to LOBs in the inter-monsoon season between February and April. That being said, maybe its climate change? I went the first week of March on my trip and the weather was a mix of dry and cloudy (though humid). There wasn't a ton of diversity on the dives from place to place (though obviously we saw a ton of tigers in Fuvamulah and encountered Spinners on one dive) and it tended to be big highways of grey reef sharks, similar to what you might find in the Tuamotus in French Polynesia but IMHO less impressive. The reefs were nice though. The dive profiles were pretty deep and we consistently ran into deco (this was my first and only time diving this way and I wasn't a fan - I think our LOB was pretty careless in terms of overall safety - in the water, on the boat etc) but otherwise the diving conditions were not difficult. A lot of drift diving and planting yourself on cleaning stations before gradually shallowing up (usually at that point we would just drive the channel into whatever lagoon and enjoy the reef life on the way in/up - we did see a couple of fast-moving sailfish on one dive which was FANTASTIC). I was very comfortable in my 3 mm full body and lots of other divers were just in board shorts.
Maldives is obviously more accessible than Cocos (where you fly into San Jose, take a bus for a couple of hours and then spend the next 24-30 hours motoring out to Cocos) as the Deep South is just a one-hour flight from Male and even down there you are doing line-of-sight sailing and are generally never out of cell reach. We had a few isolated islands visits and beach bbqs which were nice, in addition to an equator crossing party (the boat overall was very party-hardy). That being said, I had encountered a diver in Malaysia the year before who raved about her trip to the Deep South and had seen not only tigers and grey reefs but whale sharks, threshers, mola mola, hammers etc... perhaps she was extraordinarily lucky or we were just a bit unlucky in what I saw. You also generally get a lot more for your money in the Maldives - the boats are more spacious and luxurious and the LOBs are perhaps 1/3 the price in Cocos (partially due to the competition and the obvious extreme costs associated with hauling a vessel so far out to sea!). I think both destinations are worthwhile however, especially if you like big animal encounters and are a more experienced diver.