There seems to be a lot of mixed information and 10+ year old posts about this, and no actual answer that I've found, but I find it hard to believe that nobody has figured out a solution to a nearly 2 decade old Honda problem.
Ive read the 04-06 Odyssey transmission is an upgrade for the 2000-style 3.2 CL/TL, but I see loads of 04's that have trans problems. That doesn't sound like an improvement.
Ive seen newer ones that also have issues (2007 with 117k miles for example).

The reason I ask is simple; a 99-04 Odyssey in nice shape that runs great plus a rebuilt transmission is still way cheaper than a new one, but I'd like to upgrade if possible.
You can tack on the cost of a 3.2 CL Type S, the engine nicely built and swapped into said van, a couple shiny turbos, air ride, decent tires a tow hitch and a trailer for my CRX, still cheaper than a new one.
Not saying that would get done, but it would be preferable to have a solid, reliable transmission in it rather than adding another filter and a cooler and flushing with every oil change and still swapping it out every 60k.
Also, The 6mt swap is a no as I would not be the only one driving this and some people don't want to bother with the additional pedal (I still have the CRX)

 

I will retract my "junk" terminology. Percentage wise, they're not as bad as they sound, way higher failure rate than average vehicle, but volume produced vs recorded failures/complaints is not AS bad as it sounds.
For anyone interested - the "fix" seems to be repair or replace with the update that may or may not prolong it's next death.
There are a couple aftermarket kits that address some of the issues, but not much info about anyone's experience. Overhaul kits claim upgraded materials. Everyone suggests coolers, remote filters, synthetic fluid, except everyone else says it doesn't help or makes it worse.

 

4AT in my 1995 Odyssey has 175K on it and zero zero zero issues. Snaps my neck on shifts, runs cool, I keep my throttle cable adjusted nice and tight for high line pressures, and have a gigantic external cooler off some Ford Truck, no external filter, internal filter and screens never been touched. I did about 6 drain and fills and now run exclusively Honda DW1 because it replaced Z1 and is special and looks like unicorn blood. Shifting was crap with other fluids, I think they are too thick, DW1 is strangely light viscosity. Granted it's a F23 not a 6cyl.

I blame the lack of an actual modulator cable, and the TCU software is designed to be 'smooth' and not 'long life for the trans' and you can't change the line pressures by adjusting a cable (and you can't adjust the TCU code either, that I know of).

Physically the only difference I see is the "jet" kit which spews extra fluid into the guts via the service hole. The other reliability results are probably due to differences in TCU code - maybe run a TCU out of one of the years with less problems - it could have better line pressures programmed in it, less shift overlap, etc. You want "sport mode" as that is best for the trans, worst for your neck and passengers.