1. I/O isn't that bad, 40-100 GPIOs out, pretty much on par with most Artix-7 boards out there, SFP and PCIe is a plus cause Artix chips have no/slow transceivers and simply can't use them, and well everything aside from tutorials aren't beginner thing on FPGAs
2. License is pain though, you can get a proper demo license for Kintex probably
3. Compile times for barebones projects are few times more for a larger FPGAs, but as you add IPs and stuff they take a few minutes on a fastest computer anyway
But if you are not beginner some of these boards are really great. Combination of large and fast Kintex-7 FPGA, SO-DIMM, PCIe and Gigabit Ethernet is really cool. For a price of Zybo Z7-10!!! Compile time and tooling is another issue. Naked ZynQ project with ZynQ alone takes few minutes even on decent machine.
1) The boards are very bare-bones. Most of the I/Os are tied up in high-speed connectors like PCIe or SFPs, which will be very difficult for a beginner to work with.
2) The Virtex/Kintex parts they're using require a paid (or pirated) Xilinx license, and the sheer size of the parts makes compile times even slower than normal.