I think you guys are crazy. Nintendo is sitting right freaking on top of its own
Uncharted franchise with Star Tropics.
The ONLY aspect that needs to be retained from the original two games is the notion of room-to-room puzzle solving. Guess what current-gen franchise does this, and has been doing this incredibly well? Yep, Uncharted.
As for weapons and magic, give Mike a modified, current-day yo-yo like type weapon, a baseball bat, and some fire magic, and you're all set. Or just screw it all, and let Mike fight with whatever objects he finds in the environment. That could work, too. But you gotta keep it zany in a semi-realistic world with not-so-realistic monsters.
Those are really the two things that matter most for Star Tropics. But the weapons, not so much. There's free reign there. Remember, Mike even gets laster blaster type guns near the end of the first Star Tropics. Really.. anything goes.