Slumps happen.
I wouldn't worry too much, although I know it is hard not to.
The hitting experts will be here, soon, so I'll will give you another mom's perspective. I'm sure it is a matter of both. First of all, the switch from the -12 to the -3 is big. The -3 is heavier, so your son has to get used to it, and get stronger to get it around. That will happen in time, so don't worry. If he is facing better pitching at the same time, then no wonder he is struggling. They all go through this in one way or another. I remember when 2B got his first -3. He would swing 10 times and be tired. Your son will grow into it. He will get through it, and what doesn't kill him will make him stronger.
As a mom, I know you want to help him, and there are some pretty easy things that you can do. I do these things with/for my son.
1. Soft toss into a net. You can use whiffles or regular baseballs, and do it right in your back yard. Whiffles are cheaper, but he can take the swings and get the muscle memory down with his new bat. Or he can hit off a tee into a net. You can help him by putting the balls onto the tee before each swing. If you don't have a net, you can get a net for $100 online, or probably cheaper at a used sporting goods store. We also had a lot of fun with whiffle ball pitching machines.
2. Get a videocamera (if you don't already have one). You don't have to spend a fortune to get one that will do. I can't see what my son is doing "wrong" but he can. I tape his ABs, he studies them. He likes the big hits better, but when he has a bad AB, he can see what he did and make the correction.
3. If he doesn't have one already, find him a good hitting coach. We are lucky that a minor league player lives close by, and he is 2B's hitting instructor in the off-season. He doesn't have a fancy set-up, he's not associated with any "academy" or anything like that, but the guy knows his stuff. He charges $30.
Edit - floridafan is right. You can go online and get shorter (therefore lighter) -3 bats that you can't usually get at a regular sporting goods store. That may help a lot.
Edit (2) - ClevelandDad is right, too! The things you do outside of regular practice, like those things I suggested, have to be fun. My son always is the one to initiate them, and to decide when to stop for the day.