One thing i've noticed works nice against MK's is glide tossing backwards and throwing the banana down to the ground. Meta knights rarely play defensively, and will chase you nonstop. By throwing the banana down, the MK has one of several options:
1) Jump in air to try and avoid banana, but this approach is slower and easier to avoid.
2) Dash attack to pick up the banana. Easily punishable (shieldgrab)
3) Tornado over it. If this happens, keep another banana handy, or be prepared to side b. With luck, you will cancel MK's tornado, and land near or on the banana.
4) Walk over and pick it up. If the MK approaches the banana slowly, close in and prepare to either dash or grab.
5) Shorthop airdodge to pick up then quick throw. Not quite sure what to do here, but most people wouldn't think of this.
6) Pee his pant because MK is lame. This probably won't happen, but it's worth getting your hopes up.
Also, remember to watch your spot dodging. MK has such quick attacks that he'll be ready to punish you when you come out of your spot dodge. Learn to shield, shieldroll, or just plain run/jump away to avoid rather than dodging.