Samus does better offline, unless you've become accustom to the button delays.
She is a character that uses a few specific-timing moves (which are easy to time) in order to cancel the anim-lag on them (missiles, zair) which are essential to her game. Make these moves even more difficult to perform and she becomes tedious to use until you are able to have yourself compensate (which then throws your offline-game off).
On the same note though, you do get the advantage if you're able to train yourself for the lag because it makes power-shielding her projectiles that much more difficult (as someone said).