<Snipped quote by 1Charak2>
The way I interpreted the Ante Rules for this is that it wouldn't necessarily be that you'd have to give up your strongest card like in the anime, but rather than you'd both wager a card upfront before the duel began. The fact that Ammokkx said you'd register your deck and your card collection as two separate items means you'd potentially be anteing a strong card that isn't vital to your deck and potentially something that you don't even use. I can see the Ante Rule mostly being a way to get your hands on off-archetype extra deck monsters.
I could be completely off base though.
You could also just pull a Joey and lose your best card right away and have to claw your way back. There's story potential there.
Yeah, I was definitely leaving room open for people to not have to risk crippling their deck every duel. If they're in a desperate spot, though, they could always wager their key card, which would up the stakes.