Melee is faster and doesn't have a buffering system like Brawl's. When you play a lot of Melee and immediately change to Brawl, your fingers are still moving at Melee speed and you start buffering things in Brawl that you don't want to do, due to Brawl's slower-paced physics. Melee is faster than Brawl in a lot of things, and that is a fact. While in Melee the game is fast enough to not need buffering (let's say 4x), in Brawl the game is slower (3x) so what you originally wouldnt've had being buffered, in Brawl you attempt moves at the same speed, and input commands faster than what you're supposed to, accidentally setting off buffered moves. You end up imputting empty fullhops instead of shorthopped aerials, or roll backwards instead of pivot grabbing, and probably even start landing while shielding due to the L-Cancelling habits... These are some of the reasons why Brawl and Melee shouldn't be played at the same time, if you want optimum performance.
Same goes from Melee to Brawl... Brawl is slower and has the buffering system which is used ALWAYS, so when you start playing Melee you try and take advantage of that, which doesn't exist like Brawl's (you can input something 1/5th of a second before you're able to move, and it comes out). Brawl doesn't have L-Cancelling either, so you lose the 'second nature' sense of that AT. And, you start shielddashing instead of wavedashing to stop yourself from running while still maintaining safety.
Those are some of the noticeable things I've found while switching between Brawl and Melee (luckily, ZSS thrives on speed, so Melee doesn't affect her much, even less considering that my melee main is Samus and they have quite a few similarities, from the crap grabs to the dependence of tether recoveries).