This is just one person's opinion, but I only see the pre-fabbed dev boards as useful for simple prototyping. Any time I have a project, I design a PCB (stripboard is always an option) around the chip of my choice, with the peripherals of my choice. I don't think I would ever buy an Arduino (or clone) with the exact combination of chip and I/O I need, because that varies so much by what I intend to do.
Heck, half the time, even when prototyping, I just put a chip on a breadboard. Unless my needs can be met with just the pin 13 LED and a couple wires, it's less fragile on a board.
That said, for prototyping:
- The Uno is perfect for small projects.
- The Mega is perfect for large I/O projects.
- There are several good options for native USB projects.
- The Arduino team needs to implement official 1284P support like yesterday for memory-hungry (and/or large I/O) projects.
So what's left? I guess a 32-bit AVR board would be cool. Although I haven't even checked to see what that end of the pool looks like in terms of cost and features.