Strictly thinking about FPGA boards that I own...
I always liked the 50 pin headers like those used on the Digilent Spartan 3 Starter Board. It's easy to install a matching header on an add-on board. In addition, there are enough sockets (3) on the board to dedicate one to the logic analyzer (pre Vivado days).
One of the things I don't care for is the idea that I bought a fairly large FPGA (on a board) but I get just a few IO lines coming out through PMODs. Adding something like a Compact Flash to a project tends to require a lot of signals. It's nice when they all come out through a single header. Sure, I could use an SD card (and one may be provided) but the CF interface is so much simpler.
Some of the least expensive FPGA boards have the most IO lines. That's easy to do when there are no on-board features. Still, there is a place for the 'Stamp' format.
OTOH, if you want to add a simple interface, say SPI, the PMOD is perfect!
So I don't think there is an easy answer and I'll just continue to use what is offered.