I've started Smash within the N64 era and I will say that my favorite controller choice between all the Smash games is the Pro. Currently, I am using the Pro Controller due to it being wireless and functioning with a multitude of games, as compared to the Gamecube. I personally feel that the Gamecube controller is the best due to the fact that it indeed has the octagonal-carved area that houses the left-analog stick. This enables one to be more accurate with their movements and attacks. The left-analog stick also has better grip that the Pro Controller's. Negative feelings towards the GameCube controller would be the light-press function on the R/L buttons (but this can be easily remedied by removing said springs) and how the controller is so small. As for the Pro... I feel that it is perfectly viable for almost anyone to play. It is very responsive, wireless, approximately 80 hours of battery life with the ability to charge it on using many different methods, and the button layout is identical to the 3DS which many feel were quite good. The C-Stick placement is actually better than the Gamecube's in my opinion. Initially, I thought it was an awful way of placing the C-Stick but it seems to be fine for the most part as of now. At first, you may find yourself touching it by accident but that shortly stops after awhile. The C-Stick placement requires a bit less hand gymnastics as compared to the GameCube controller's layout. Like I said earlier, my complaints on the Pro controller are the lack of semi-circular grips on the analog and the lack of octagonal carving that in which stunts your movement and accurate inputs, but that seldom happens and isn't that big of a deal when you get used to the analog placement. I personally have not held or used one before, but the HORI Fight Pad may be the best of both worlds. It's semi-wireless, apparently little input-latency, has the octagonal carving, multi-circular grip, original placement of buttons from the GameCube, has an extra shoulder button, digital press shoulder buttons, decent aesthetically, and the price is quite fair for these, assuming you buy them from retail rather than re-sellers.
As for the other controller options....
The GamePad is fine for what it is. The battery life is awful the the weight may bring you down a bit, unless you get used to it, which in my case, I did prior to converting into the Pro controller. It is also very wide, but easy to get used to.
I used the Wii Mote + Nunchuk pair for a long while and it isn't as bad as what many may it to be. Sure, there is no C-Stick and has a bit input-latency, but really, it isn't as bad as some other controller options. Personally, if I had to choose, I would stay away from this as other controller options seem to be significantly better. Having to hold two controllers that are wired together isn't very ergonomic since having a set hand placement is always best.
The Classic is actually quite good. I've seen people pull off great things with it, but I'd say it is not as good as the Pro or Gamecube. I have used one before and it handles itself find. I am not a fan of the shape but for those who are, then it should be an okay controller. Have seen someone in the competitive scene use this.
The Wii Mote is just awful. The D-Pad hurts my fingers and characters feel very stiff when using it. Also, using the trigger as an option isn't very ergonomic. I do not recommend this controller to anyone unless they've already used and have adapted to it. If you use this, you will likely lose to others who have better controller options. Sorry for those of you who read this and are "good" at Smash or actually prefer using this. I really can't see Smash being that playable with the Wii Mote. Sure, platformers are great with a D-Pad and few buttons, but Smash takes better movement options since platformers are so linear.
Tl;DR HORI Fight Pad seems to be the way to go. I personally do not have one currently but will eventually get one so I can play PM on my Wii U without having to use the Classic or Nunchuk pair.
Also, it breaks my heart that no one has mentioned the DK Kongo drums... You can certainly play Smash with it. I've used it when I played Melee for the jokes. xD... It isn't viable at all but it's very fun. I think the sensor picks up your claps as Smash attacks? Forgot since it has been too long.
But all in all, one should never discriminate another controller option since it all ultimately depends on the user than the controller itself, I can't say this is the most true to the Nunchuk and Kongo drums, but the majority use the other controllers.