The thing is I HATE the N64 controller, the analog sticks always fail, and they are uncomfortable. For most games you dont need the 4 C buttons, on the face, they are usually used for moving the camera around, so i just mapped them to the second analog stick. For the few games that use all 6 face buttons though, its annoying.
All a matter of taste of course, but for me, if I could choose only 1 set of retro ports to add to my arcade cabinet, and I wanted maximum versatility across all consoles and arcade games... no contest whatsoever... N64. For my money, absolutely the most versatile of all console controllers, FOR EMULATION PURPOSES, when coupled with a program like JoyToKey. Allow me to convince you beyond a shadow of a doubt...

1) Seamless mapping to standard arcade control panel. Button A, B, and the 4 yellow buttons line up just like a standard 6-button control panel, and the D-pad maps to your 8-way joystick. Why would you want to replicate a control panel on a controller? I see two reasons - first, some (younger) players generally prefer the D-pad over the joystick, and this allows them to play classic arcade games with a controller they can relate to, and second...
2) Allows for simultaneous 4-player arcade action on your 2-player cabinet. Alternate controller mappings can be loaded into JoyToKey via batch files, which can be launched from most front-ends. One such mapping could assign the default MAME Player 3 and Player 4 keyset to your N64 controllers... now you have two players on the control panel (Player 1 and 2), and one on either side using N64 controllers (Player 3 and 4). Think NBA Jam, Gauntlet, Simpsons, etc. etc. I have your attention now, don't I

3) Focusing on console games, each N64 controller provides a total of 10 buttons, one D-pad and one analog joystick. True, this does not cover dual-analog systems such as Playstation, but it covers all the classic consoles pretty well (unless you're a big Atari2600 or C64 fan... that calls for another set of retro ports). And if you're a fan, as a bonus, you get to play N64 games with authentic controls.
4) Flexibility... coupled with JoyToKey or similar software, the analog stick and button Z (trigger) can function very nicely as a mouse and left-click button while in the front-end, playing PC games, or simply navigating in Windows. Also, with 10 buttons per controller and very few systems requiring them all, you can set up one of these buttons to function as the "Shift" key, which when held down, remaps all buttons to an alternate keyset. Use this in the same way you use your keyboard encoder's Shift function, to give yourself access to Pause, TAB, Enter, Tilde, the Function keys for your computer emus, etc.