You're being charged to maintain a cloud service into the indefinite future and ensure it's compatibility with pokemon titles for years to come. If you think you're so entitled that that technology should just come to you free than you're an idiot. Cloud tech is expensive and running a system like this for the amount of traffic it will get costs money. Money that's not just going to pop out of thin air. Five dollars is nothing for what they're offering and if you don't like it just suck it up and do it all at once during the trial.
It's not like it's a webpage that has ad space to generate profit, it's on the 3DS, they'd literally be at an extreme loss if they didn't charge