I don't think this is isometric, looks more like an oblique projection.

The idea is cool, but I think the overall visual result is rather underwhelming because each organelle(?) is so small relative to the tile. The tiles also have a lot of thickness but the organelles are confined entirely to the top surface, looking rather flat as a result. I think making them a little larger and letting parts of them be obscured by the front wall would look more impressive. I think more volume would be good too - this isn't going to be realistic anyway, so don't be afraid to exaggerate and stylise to make things pop and look more interesting.

They don't look very biological. Real life cells have a lot of stuff suspended inside the cytoplasm, including bubbles. And you don't need isometric or oblique projections unless your game's playfield is actually 3d and objects can have Z coordinate, or you're making an RPG game, and the angle is part of the genre and used to set up the mood (i.e. more mature Fallout type RPG, instead of light-hearted RPG maker games). I suggest getting rid of the hex prisms, while retaining the soft looking grid and some overlay to show stuff like bubbles. And instead of XY plane, use the XZ plane, and so it will look like this slime (not mine), but with hex organelles inside:

There is also a special kind of orthogonal projection, called skewed isometry. Basically it is a an isometric projection scaled 2x and rotated at 45 angle so that the diamonds become squares, which allows tiling them easily with the simpler RPGMaker like engine, without actual isometric engine, while at the same time directional movement is more intuitive: up is still up on d-pad, and north is north. It is a bit easier to draw some art assets in this projection, which gives the distinct artsy look, while maintaining the proper isometric engine 3d capabilities (Z-axis can be visualized easily). It is nauseating to look at for RPG games, but could work with a bio-themed game.

It can be produced in several ways. Another is rotating the proper isometric render by -15 degree, then skewing/sheering 2x (Nth scanline moved 2N pixels to the left).