PS: for the 3d models' textures, I would suggest to run them through a pixalator so the look & feel is more coherent, there are tools for that or even possible via photoshop. If you like I can help with that if there is a way to access or get the orginal textures;)
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I think you hit a great balance with what you chose to modernize and what you chose to keep the same. If too much was done it would lose the charm and feel of the original game. The excellent pixel art work on the wall and floor textures really defines the game so keeping it in preserves that.
I really like what you did with the monsters. They feel close to the original pixel art and not out of place.
And some of the touches you added are great. I love the way the water octopus dies for instance