Is there more to Johannes than meets the eye ?

No - you're not the only one feeling paranoid about Johannes. He just gives off a certain vibe that he knows much more than he is letting on and may have ulterior motives. Dominique's statement in her first cutscene "Oh, do you decide for her then?" only cemented my opinion. This is a good sign though; I like characters with a bit of depth.

I've actually always pegged him for last boss. He's as unassuming as they come, and too closely related to the two main characters not to play a pivotal role. Going by past Igavanias, we pretty much know Gebel's not going to be the real last boss. Alfred's too obvious a candidate, so that leaves Johannes and ... Dominique as my second choice (because there's never been a Japanese game where the Church has not been up to no good).  My money's on Alfred replacing Johannes at the alchemist shop when the time comes.

Don't forget about the controlled by a demon cliche (Gremory)
honestly i don't think Johaness will betray Miriam, he obviously knows what happened and may have his reasons to keep it all as a secret but i refuse to believe he is a bad guy.
As for Alfred im pretty sure he will get his hands on the book, maybe summon a demon and fuse with it then get killed by someone other than Miriam, also i remember Alfred's voice actor saying he would tell Alfred to watch his back if he had the chance. (spoiler: Alfred dies)
Dominique miss bananas hair looks like she will be the character that will support miriam with the HOLY POWER! i don't see her as a posible enemy unless she tries to stop Miriam if she ever goes demonic but Zangetsu is there for that.

leave my boy Johaness out of your evil plot twists >- >

Johannes reacting so quickly to Alfred's presence and getting to the castle without help was a little suspicious. But there's something about Anne, too. I wonder if she's Gremory in disguise. Something about her necklace somehow brought to mind that idea. Well, that, and the fact that she's hanging around a ruined village.

Johannes get wounded. Alfred gains power. Gebel is dying. Go Miriam Go!

Anne takes over for Domi when she's away from the shop 

Another character could replace them at their stores, though.

And I don't know if Anne's actually the last boss, but she's definitely the creepiest thing in that demo, lol.

You can thank her English VA for that, who tried to sound like a child, but ended up sounding like an old lady.

It's worth noting that her Japanese voice is pretty fitting for a child. It's what you would hear out of a loli character in anime.

You can change the language in the beta demo by pressing all 4 shoulder buttons at the same time.