For a blank PCB this small, you can get 20 made up at Seeedstudio for around $40, depending on the shipping method you choose. The smallest board they offer is 5 x 5cm and you get 10 of them, and 2 of these can fit per board at that size. As far as the time it takes to design and such, I did the entire thing in a few days in DipTrace really from tracing out the CL board, making the schematic and figuring out how I wanted it setup on the board and then doing that work. The Wired CL controller is fairly simple, by comparison to the other versions anyway, and it was a good solid few days of work too, not a couple hours here or there.
As far as making it 'easier' goes. If you had all of the smaller common parts pre-installed, then went to install the 56 pin QFN IC there you'd probably loose a few of the smaller ones in the process, and if you can solder a 56 pin QFN with no issues, then you can solder up the rest of the parts with no problems at all. You'd also have to know the value of every component, and while checking Resistors is no big deal with a DMM, you really need a Capacitor and then Inductor tester to get the values from those parts (which I don't have) whereas they're already the correct value and right there on the CL board to be removed and swapped over to the miniCL.
Not sure which PS3 Daughter board connector version you're considering? There are only 2 that I know of, but each one has it's issues, depending on what you're trying to do with it also. http://forums.xbox-scene.com/index.php?showtopic=648322
The older style plugged into a connector, and making up a 'go between' board for it would be kind of pointless since those older version controllers already have TP spots on the main board for everything. These are the ones used to make the 3PS60 controller in this thread as they use the older 10k POT style Sticks. Even though it has TP spots, the Daughter board itself still has to be altered for most things as it's button contacts are Resistive for the Analog functions of the PS3 controller, so they don't work as Digital until that trace is severed.
Now on the later version PS3 controllers, the Daughter board connects a different way and a 'go between' board could be pretty useful, but, those version controllers also use the newer Hall Sensor Sticks, which can't be used with anything but the PS3 controller without doing some more work, so it would only be one step in that process.
The latest version PS3 controller board, the Asuka, has gone back to using the 10K POT style Sticks, so a 'go between' board for that version could be useful if making a 3PS60 controller, though making it a PCB would be pointless as it would be too thick to put in there, unless it was made up as a flex board, and those don't really like to be soldered on after the fact.
I kinda see where you're going with that idea, and it's a good one, but if you were going to make it a PCB then it may as well just be a 'blank' PS3 controller PCB, like I did with the 36X board. viewtopic.php?f=56&t=51111
But even that would be pretty futile since some of the different revision boards aren't swappable between shells, so you'd have to make it specific to some version or another, and then the only Sticks that fit in them are the ones made for the PS3 controllers. Those things just weren't made to be hacked on easily.
It only costs me the price of the PCB, a CL controller and then my time to swap all of the parts over.