Best way to deal with change ups is to not swing at them. I don't know how familiar you are with baseball, but a change up (and off speed in general) is a pretty situational pitch. Know when to expect one, lay off if you can. Same goes with pretty much any off speed, don't swing if you can. My RTTS guy is tearing it up in AAA right now, I pretty much just take pitches until I see the one I want (belt high and up fastball or slider).
You generally won't see a change on the first pitch. It's usually used after a couple fastballs as a strike out pitch or to get you to ground out. Double play situation? Good chance you'll see a low change up or sinker. If it's a pitchers count (0-1, 0-2, 1-2, 2-2), your chances of seeing a change up go way up. There are some pitchers who throw a lot of change ups, though, so watch out for those guys.
You can refuse to use the guess pitch feature within the game, doesn't mean you have to stop actually guessing what pitch is coming based on the situation. To really "deal" with change ups, you need to work counts into your favor so you see less of them, even the best get chewed up by off speed pitches in unfavorable counts. And then practice just not swinging at shit like a low change, guaranteed ground out 3 of 4 times.