A tricked out KDX will be easier to ride, but a 125 (or 144) will be faster.
I have a 220 with the following -
FMF Rev pipe
FMF Turbine Core II silencer
Boyseen Reeds
FPR Porting
FPR cut head
FPR bored carb
Cut up airbox lid
13/49 gearing
Proper jetting
.40 kg fork springs with 7.5 wt oil
A fresh 125 with a pipe and proper jetting can give me a run, but I almost always win. In fact, the only guys that run neck and neck with me are between 30 and 45 pounds lighter (I'm 180ish). I've never ridden / raced a 144, but I'm sure it would beat me.
I have friends with 125's (98 CR, 01 YZ, 03 YZ, 03 CR). We trade bikes around, they always are amazed at the overall pull my bike has, allowing them to shift far less. But they are horrified at how "fat" my bike it. It really does feel like riding a sofa compared to a 125er. All of em say it's an easy bike to ride, but too hard to go fast on.
When I hop on a 125 the first thing I notice is how tiny the things feel, like I'm on an 80. Second thing I notice is that I have to keep it screaming to make foward progress. I'm sure a 144 has much more low-mid than these bikes though. After a minute or two I'm used to it (I rode a 94 YZ 125 for years). Then I wonder why I have a KDX. I can flat out haul the mail on a MXer compared to the KDX on pretty much any terrain.
In whoops it's no contest. If I'm swapping ends on the KDX at 30 mph I can be calmly cruising at 40 in the same section on an MX bike. Granted a revalve would help me a lot, but I don't think it'd make up that difference.
In single track stuff the 125's are a blast. As long as you are willing to use/abuse the clutch you can fling them through area's where the KDX is bull-dozing me around.
In super tight stuff (like barely moving, crawling over logs/rocks/other riders) it's more of a toss up. The KDX is easier to keep running and moving, but the 125's are much easier to man-handle over obsticles.
On big wide open trails the KDX wins. My bike will pull over 80 mph on GPS, so I eat those guys up. If you geared a 125 to do that the gap between gears would be horrific.
Now, for casual riding the KDX wins. I can cruise all day, no problems. Putting around on a 125 gets old after a while. At race pace my bike beats me up and wears me out, where as a 125 is lighter and eats up terrain better, letting me run hard longer. If I had to do it over again I'd buy a KTM 200 or a 250 motocrosser. To me that'd be the best for running hard, yet having enough power spread to cruise around comfortably when need be.