Has anyone found any interesting boards that are not just clones of the Mega and Due board?
For reasons that I don't understand the vast majority of today's boards have a relatively low number of pins which is a problem in real world projects. Something like the SAM3X8E processor used in the Due seems to have a lot of interesting features compared to the SAMD21 line.
I've just ordered one of the ST Nucleo eval boards that supposedly has a set of headers compatible with an UNO shield. It also has additional headers for some of the ST plug-in modules. I don't think it has as many externally accessible pins as a Mega.
When I need more memory and a lot of pins, I use ATmega128 - Flash 128kB, RAM 4kB, EEPROM 4kB, IO pins 53. Since there is no suitable board, I use ATmega128 as a stand alone chip - the price is much lower.
Probably not so many as you are interested in, but the Teensy 4.1 has a good number of pins in a compact form factor:
https://www.pjrc.com/store/teensy41_pins.html
For a lot of real world projects, UNOs and Pro Minis are just fine, which is why they are popular.
When you need more pins, a bit more memory, more speed and 3.3V operation then the DUE fits the bill for me.
If I want just a few more pins (vs ProMini etc) I go for the ATMega1284P, 8 more pins than a Pro Mini, very low power sleep, 4 times the flash and 8 times the RAM, available in 40 pin DIP.
There are the STM32F Eval boards (nearly all of them, these days, I believe?)
How about "Wiring", using the ATmega128 (and etc)?
The biggest "problem" is that there doesn't seem to be any commonly accepted pinout that is "bigger than an Uno and smaller than a Mega" 
(or "bigger than a mega", either.)
I have made Atmega2560 boards that break out all 86 IO pins, vs the 70 the Arduino brings out.
Also a 2561 board that has 54 IO.
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