I am using the "tray" idea you have and find it works very well. In fact I have converted from all of my multiple "traditional" tackle boxes to one of the new tackle bags that holds trays. The bag I have is a Flambeau, but many companies make them. It holds 4 trays in the bottom and more on top. Also has side pockets for extras.
The really nice thing about it , besides only needing to take out 1 tray at a time is the versatility. I can trade trays depending on the season, water-level and species targeted. There is always some basic gear that I always carry, but some other gear trays I swap all of the time.For example in the fall I may keep my normal drift fishing tray in the bag, but I would swap my steelhead plug and spinner trays for trays more geared to kings/silvers.
It is the best tackle organization system I have been able to come up with. It really takes up no more room than a medium sized tackle box, holds mnore gear. It really beats reorganizing my tackle boxes every season/type of fish. And it definately beats a soggy, cumbersome vest in a drift boat.
The only suggestion I might have if space is really a factor is to totally minimize and just carry 1 tray or a couple. I feel the need to be prepared with a full array of different types of tackle, so the little bit of space taken up by my bag is a small price to pay.
Something to think about though is how much gear you and any partners bring into the boat all together. It can be overwhelming in a drift boat if three guys each brings a full load of all their favorite gear. Coordinate so you don't have multiple of everything. My partners and I each bring a small amount of our own drift/float tackle, but the guy with the boat brings all the plugs, plug rods, etc.
My .02$.
GS
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"It's NOT that much farther than the Cowlitz!"
"I fish, therefore someone else must tend the cooler!"