Maybe I don't have enough experience with high pin count devices, and this is just normal, but the 407x/408x pinout section is probably my biggest gripe. Dozens of pages in a table format of all the possible pin functions, in port order. There are no cross-references in pin order (probably because there are 7 different packages and that would be a lot of tables) if you just need to know what pin 27 does for e.g., and no section (that I've found) that will tell you what pins provide MII / RMII, UART, SPI, i2c, CAN, etc... You gotta scroll through the whole table, pages 11 - 50. (Or, preferably, just use search. Not very friendly on a phone / tablet.)
They do at least provide a pin mux tool. Except it doesn't cover the LQFP100 package.