Caveat: I haven’t owned either Maltron or Kinesis Advantage, but have only spent a few hours here or there typing with them (so note: not fully fluently).
Top level conclusion: I definitely preferred the Maltron to the Advantage. The biggest things were the step/angle on the pinky keys, the stagger/step on the middle finger column, and the orientation of the thumb keys.
On both Maltron and Advantage, I’m not a big fan of the orientation of the number row keys, I think they angle forward too much. Better in my opinion would be to have narrower keytops closer spaced along the columns (e.g. 17mm instead of 19mm) with a similar height step between rows but with a more vertical switch axis on the top rows.
Also, I think both keyboards should have added another couple of index finger keys on each hand towards the middle of the main letter block, scooted the pinky column slightly toward the body, and maybe ditched the top outside corner keys and bottom row pinky keys.
The Maltron thumb section overall isn’t ideal (several of the the 1u keys are a bit awkward to press), but the two big keys (space and E in Malt layout) have great placement and great orientation. Probably the most comfortable spacebar on any keyboard I’ve tried. The other thing the Maltron is smart about is putting a vertical height step between different finger columns. This reduces the amount of horizontal stagger required to make these keys comfortable to press, allowing the text block to stay closer to rectangular.
The designers of the Advantage mostly copied the Maltron layout, but I feel they somewhat missed the point of the Maltron’s placement and orientation on the thumb keys and the step/orientation of finger keys. I think the Advantage would benefit from scooting the middle finger away from the body and pinky finger toward the body and/or lowering the middle finger column and raising the pinky column, and tilting the ring and pinky finger columns so they’re more aligned with the other finger columns instead of oriented outward to match the “bowl” shape. I also like the tall shifts on the Maltron better than the slightly wide shifts on the Advantage. The thumb section in the Advantage is okay, but it’s noticeably less comfortable for me to press the main spacebar keys than on the Maltron. The overall hand position required on the Advantage is a bit less relaxed, in my opinion.
Personally I would ditch the Maltron’s central numpad, and just put numpad functions on the main section of the right hand, on a layer. I’d also ditch the F keys and put those on a layer, but I can understand some people need dedicated F keys with clear legends.
I don’t personally think either the Maltron or the Advantage does a great job with placement of modifier keys, and I don’t much like the treatment of numbers and symbols on any of the “standardish” keyboard layouts (including QWERTY, Dvorak, Colemak, Malt, etc.). If I had to use the same physical key arrangement as one of these keyboards, I would heavily customize the logical layout to match my own preferences.
Versus keyboards with flat halves like the Keyboardio, the Maltron definitely has some advantage by being sculpted. In particular I think having a different orientation between finger and thumb keys can be a nice improvement, as is having different heights between fingers. The keyboardio can make up some of the difference via carefully shaped keycaps, but it’s still not quite the same. The split design of the Keyboardio/Ergodox/Matias ErgoPro/IBM M15/etc. shouldn’t be underestimated though. Everyone’s body is a little bit different, and likewise there is great variability in desk/chair setup. If the two halves are independently adjustable, you can move and orient the halves to minimize strain on your muscles/tendons much more than any one-piece keyboard allows.
Recommendation #1: don’t take any of our advice as gospel, but try them all for yourself. YMMV, etc.
Recommendation #2: try not to get sucked in quite as much as obra did. The next 5+ years of your life don’t need to revolve around keyboard ergonomics.