You can plug in Gamecube controllers in the top of the Wii but you can only use them on Gamecube games and selected Wii games. Check for an icon of a Gamecube controller on the back of the game's DVD case to see if you can use it.
On the whole though, you will have to stick with the Remotes. If you are having battery troubles, many game shops and online outlets such as Amazon sell docking stations for the Wii, which plug into one of the USB ports on your Wii and charge your remotes from the Wii's power. They retail from $20-30 (I think), but it's miles cheaper than constantly using non-rechargable batteries. Even if you already use rechargable batteries, it's much easier just to plug them into overnight and be fully charged in the morning.
Hope I've helped!
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