I've jumped around a lot. All of this info is biased around me using Lucas unless otherwise noted
I tried to play through SSE with the Wiimote and Nunchuk, but after having difficulty in the first battle, I decided that I would use the Gamecube controller just to power through single player, as I wanted to beat it quickly. My first few wifi matches used this controller as well.
A day or so afterwards I switched to the Wiimote and Nunchuk combo. I experimented with shake to smash a great deal, thinking that in theory it would be able to replace the use of a C-stick. I bound Z to shield, C to grab, and Down on the D-pad to jump. I was moderately successful with this scheme, and noticed that it really helped me to use neutral moves more often, jabbing and my N-air.
Shake to smash was really... not good though. I wanted something a little quicker to preform some precise air moves so I bound the side and up buttons on the wiimote d-pad to smash, allowing me to use my up air and forward air better, and get quick smashes off on the ground ( People really like running into a bat attack if your not facing them). I tested the " Wiichuk 2.0" scheme with and without shake to smash, and eventually decided to drop shake to smash as often it would read my input wrong and I would get punished or miss a kill for that reason. Over time, however, I realized that using this control scheme made me loose one of my best offensive tools, which was jousting with a down air.
To recap what jousting is for people who are not familiar, its using a move in a way that it attacks the opponent, but you continuously move while using it, so its much harder to punish. While in Melee this was always down with air moves, a good example now would be Wolf's forward smash. Lucas's has multiple hit boxes that catch the opponent, so you can either tag them with it and do more damage, or hit with only one box and land safely, so it really gives you many options. If you just do a down air with control stick input, you always gain downward momentum, but via using the c-stick, you can do one while moving up, or horizontally.
So with the lack of being able to joust using my down air, and loosing the ability to play my melee main, Jigglypuff, whom I need a c-stick for, I decided to switch back to a traditional control scheme. I considered going back to a gamecube controller, but I decided that I didn't want to over-ride the muscle memory I built up for melee ( Using tap to jump as opposed to using another button). So on Thursday I went out and purchased a classic controller.
With the classic controller, I've noticed that in general it responds faster than the wiimote combo. I also find the extra shoulder button and the placement of them to be a large boon. I was initially disappointed that I couldn't use the d-pad to move, but I quickly got over that. All the buttons feel good, though the Z buttons can be funky, having a 'click' like a mouse press rather than the feel you get from most buttons. I've experimented with setting the right analog stick to tilts and B moves.
I am a large fan of the tilt stick, and think that if it's inputs were more precise that it would greatly help my game, but, due to the fact that it accidentally causes jumping and neutrals, I'm slightly disenchanted with it. While getting off more reliable and quick up-tilts and forward tilts is nice, one of my largest gripes is that I cannot do a forward tilt in a direction I am not facing, unlike with the C-stick.
The B-stick was interesting, but ultimately only useful for Lucas' wavebounce. While easy to pull off and immediately useful with defensive applications, the timing for actually firing a pk Fire at an angle that will hit a grounded opponent is very difficult to get, and I loose one of my strongest tools, which is air moves without transferring momentum.
I really with that we had a MMORPG level of customization with controller set ups... I would love a controller that had 2 right analog sticks, and better shoulder buttons. Ultimately though, I think that the classic controller is the way to go.