I am printing a wheel with a 2.5mm hole in the middle to accept a shaft of a motor with a set screw. The problem I am having is that the wheel is always wobbly when spinning (sometimes more, sometimes less without changing any parameters). Is there anything I can do to make this print as perfect as possible and prevent the wheel from wobbling?
3D printing bores/holes is inherently and wildly inaccurate. You can continuously tweak the model, material, and print configurations to get better results, but for best results, in my experience, redraw the hole to a slightly smaller size than your target and reprint. Then, after printing, use a drill to get the size and geometry more precise.
For your case, re-design the hole in your 3D model to 2mm-2.2mm and use a 2.5mm drill after it's printed. Make sure with your infill amount that after drilling you still have a solid hole surface(infill is not exposed) Also, if you have a drill-press, use that for better drilling results.
Also, the plastics used in most hobbyist printers are really not well suited to carrying any load and are usually too soft and flexible to machine properly.
However if you can find a piece of tube, either metal or rigid plastic, to fit the axle accurately, design the wheel bore so that the tube can be pressed in. It should be a snug fit. Screws, glue, etc can attach the axle to the tube.
When you say the wheel is "wobbly" do you mean that the bore is not aligned with the tire along the axle axis? Or is the bore offset from the centre somehow? Can you can share your design so that we can understand the problem more clearly?
Here is my solution for those with similar questions - cut out a small portion of the part (in the model) and print that. Replace that part with a piece of wood that fits the cut out, and drill into the wood instead. Attach them together with either screws or glue (don't use CA with ABS).