I only really ever use ender chests to pump things out into a sorting system so I think 9 slots is enough. Also, it's good that you can have multiple ender chests with different items.
Not for me, I like to build processing plants that can handle huge peak volumes, my last major build could process* in real time the output from 24 fully powered quarries. To do this I had to design and build item/flow regulators and much more besides, the ender chests as a 3x3 is way too small a buffer space, it could be filled in one tick (and would extremely like be filled in one tick) and I need a space much larger than that per tick (i.e. even if I empty the entire chest every tick, in the very next tick there would be more items than the 3x3 could hold, so my entire system would backup and be limited by this bottle neck.)
I'm thinking of other designs, which is cool I guess, but what I intended to do with my next major build was to push on to being to handle in real time the output of 64 mining turtles each mining one chunk.
The problem so far, is that every design I've come up with so far that does away with or deals with the ender chest nerf will cause way more server load.
*sort, macerate, sort, furnace, sort, do something with stuff, sort, autocraft, storage etc
Yeah, my biggest extractor (as I called it) had 4 ender chests all with 6 sides with retrievers, in normal operation I only pulsed this once every 2 seconds which was more than enough, these then fed into a regulator I built, which consisted of two sorters, 2 diamond chests and 8 retrievers, basically all this does is make sure that the items most regularly flowing through the system are stacked before entering the tube network properly.The chest should have 3 times less storage than before. So just use 3 chests with equal distribution instead of one. This would be easy with redpower and it should be doable with logistic pipes.
Enderchests from Chikenbones are pretty useless now anyway, nerfed them down to 9 slots and no config to change them back to useful.
I used to use them extensively in my builds as teleport pipes/as a way to prevent me having to run huge long pipes, but it seems I should be going back to the old ways now.
I find Redpower tubes and Retrievers are best, they too pull out a full stack, but stop pulling if other parts of the system are jammed. The regulators I built regulated 60 plus different item types, not just cobblestone. It would be cobble stone that causes the problem, except I can actually deal with it very fast, in the build I've been talking about, I pumped it into an array of Energy Condensers transforming into wood, which I then pumped into furnaces turning it into charcoal which was then used to power generators, any overflow (i.e. too much supply of cobblestone) flowed into a final array of Energy Condensers which condensed into diamonds.In that case pumping out with Buildcraft could be more effectiv. A Stirling-Engine pumps whole stacks out, and if you sort them (Cobble out basically) you could distribute it nicely. I guess it is the Cobblestone that jams you system, so sorting it out via Buildcraft should work a bit faster. After pumping it into two Chests you could use Redpower to move on.