It's actually pretty easy if you plan your moves out instead of just matching the first thing you see. Protip: Pay attention to what possible moves you're giving the opponent. The AI will always prioritize attacks over everything else, and this is easy to exploit. You can set up 4/5 of a kinds and combos of other gems that they'll ignore, and you can bait them into attacking you while you have defense+counter up. Just focus on controlling the board.
Pressing down looks like a blocking pose, but doesn't appear to actually do anything. And it seems enemies don't get any hitstun at all, contrary to what the lying combo counter tells me. Also, this needs the specials that have become a staple of the 2D fighting genre - a fireball and a startup-invincible DP-type reversal. Look at some other established fighters and take notes, because as it stands this is kinda just a strategyless masher.
That indicator of the boss's position at the bottom of the screen is an extremely helpful touch, brilliant idea. Never have to worry about take my eyes off my character when there's too many bullets to do so.