I only have the Kinesis, but....
The Maltron is the original, and is a hand-produced, which is why it costs so much more. The Kinesis is a mass produced alternative, based on the Maltron design, with a few improvements and a few downgrades at the same time...
The function keys on the Kinesis really do suck (this is pretty universally agreed upon), but they are usable.
You are likely to decide you want to remap a few keys to suite your personal preferences, particularly given the alternative layout. I've found the hardware programmability of the Kinesis very valuable for this reason (the Maltron doesn't have this feature).
The Maltron angles the hands down about 30 degrees from horizontal, vs 20 on the Kinesis. Furthermore, the thumb clusters of lower down on the Maltron. Thus, the Maltron's layout is considered a little more ergonomic/comfortable than Kinesis's by people who have used both. Having said that, most of us ergo-geeks tend to prefer the lighter action of the Cherry brown/red switches found in the Kinesis vs the Cherry black switches in the Maltron.
If you do any gaming, you might want to go for the Kinesis, as it has 6-key rollover (up to 6 keys can be registered simultaneously without interference; this is the limit of the USB keyboard protocol, so you'll find 6KRO on most high-end keyboards).
Overall, I think you'll be quite happy with the much less expensive Kinesis.