Whoa, a spiritual successor to The Guardian Legend! I never did get around to beating that game...
As others have said, the gameplay is solid on both fronts. The only things I think could be improved are 1) more enemy shot patterns for the shmup segments (a few enemies shot directly at me, but that was it; most were on innocent joyrides before I swooped in and murdered them), and 2) the lockdown rooms in the Zelda segments should stay empty after being cleared instead of relocking and respawning the enemy waves if the player dares to get turned around. The boss was also very easy, so if you won't change its pattern, maybe lower its HP so it takes one or two fewer hits to die. Also, maybe make the sword deal more damage to enemies so it has a use besides breaking the crystals.