One thing you can do is practice a set of combos like say you're using Luigi - keep in mind I don't really know his combos, so I'm just giving examples. All right, so start off with a D-throw to Uair to Fair. Add in a couple of other combos like D-throw to Nair to Bair or D-throw to Nair to Dair. Keep practicing thing so it's like second nature. It's like what Bruce Lee said: "I fear not the man who has practiced 10,000 kicks once, but I fear the man who has practiced one kick 10,000 times."
The unfortunate thing about SSB is that it doesn't have trials like in Street Fighter, The King of Fighters, Marvel vs. Capcom, etc. where there's preset combos the developers put in for you to challenge yourself and work on inputs, timing, and stuff. Would it have been nice to have something like this? Yes, but SSB does reward you for finding out combos and doing things on the fly and knowing that something works. Oh, an opponent is taking some time to recover, well, use Falco's Dair on him or an opponent will probably roll behind me, use Ike's Down Smash.
Another option is to customize your controller. Some people work well with default controls; some don't. In some cases, it's actually more beneficial to modify the controls. In DMC4, Nero's Charged Shot is very useful for his combos and approaches. Well, people ended up mapping Shoot from Square to R1. Likewise, in DmC, Dante's Richoshot allowed him to lock enemies in place, so people mapped the Shoot button elsewhere. Hell there are people who play games using entirely the shoulder and bumper buttons for attacks and leaving the face buttons for jumps and such. Speaking of which, a DMC player by the name of Sam D made it so Square was Attack and X was Jump allowing him to "piano" the buttons and perform Jump Cancels easier.
It's one of the reason why people prefer playing RPGs on mouse and keyboard because of the customizability.
