The controls are unorthodox more than anything, and that's not necessarily a bad quirk. The game feels remarkably tactile because of it, and it would've felt a lot less satisfying to play if the devs went for something more typical. I mean, it is what it is if it's not your cup of tea, but it's not the game's fault if you feel like you're flailing about.
Agreed, just got up to episode 3 and I really enjoy the controls after spending a lot of time dying and learning from my mistakes. I'm mostly always in mech form, and then switch to the airship as a last resort for missiles. A trick I use is to hold square and charge your sword attack at the same time and evade as you go in for a strike. You can also grab enemies and strike them while holding them.
If you haven't unlocked the mech form yet, get used to using the roll ability to evade missiles. If you're facing multiple ships at a time, use your agility to make them hit each other. Try your best to collect & buy laser upgrades. The L1 strafing is helpful too.