Considering I graduated HS over a year ago, I'm not so cautious about it so much anymore. I can walk around in a store with Pokemon in my cart, no problem. I was always known as the Pokemon Freak/Nintendo [Insert Insult] guy through middle and part of high school (until I transfered schools). I would never talk about it openly or anything or when I was asked about it I would deny it and say, "What? That stuff is for children. Lame." Buying Diamond in the store made me so nervous (HS Junior at the time) or buying the cards, I would constantly look around making sure no one saw me (very very stupid looking back). Now I will just walk in, buy a game or cards and think nothing of it. Platinum was not hard at all and two little kids bought the game right before me in line!
How some high school kids can like Hannah Montana/Disney Channel crew and listen to the music and be fine to show it and people think nothing of it, yet kids that like Pokemon (and anything anime in general usually) get picked on baffles me to no end. It doesn't add up in my book. Pokemon is no different to it or Star Wars, Transformers, Marvel Heroes, DC Heroes, etc. They are all marketed to appeal to all ages. You can find Playskool Star Wars toys and Spider-Man shoes for toddlers in any store.
Trust me, when you get out of HS, you will look back and find it all very silly. The popularity contests, trying to act cool by any means, etc. doesn't mean squat when you get kicked out into the real world.
That's because in the real world, no one cares if you were captain of a ball team, prom king/queen, uber popular, a geek, nothing. You are just a person.
I know it sounds like an after school special, but it couldn't be more true. I was quite popular my senior year at my new school, but I never talked about Pokemon or anything (not even video games). Don't flaunt it around or anything, but if you want to, go for it. There's a time and place for everything. Like with acting, keep stuff on the stage, don't bring it off.
There was this guy in my art class who was a MAJOR (and I mean MAJOR) Halo fan. Everyday he wore a Halo shirt (usually the same one day after day), would drink the Halo 3 Gamer Fuel soda, and talk about his... disturbing... love for Master Chief. He had Halo themed pins on his tux for prom even. But he was very annoying talking about Halo nonstop for 9 months in class. Him and me were the only guys in the class too, so I had a lot of girls to talk to actually.
Don't let other people control your life, because you will always have haters. Trying to please everyone, you will just break your back doing so, so don't even try. Do what you want. Participate in the hobbies you want to. Enjoy life how you want. High school popularity means nothing when you enter the real world (but when I say that, don't totally destroy your social life and dedicate yourself to one thing to where it's annoying).
I probably typed that as a mixed signal mess (it's late and I'm tired), but overall: Like what you want, don't worry about the judgment of others. But keep in mind there's a time and place for everything.