Welcome to the Tank!
What kind of substrate were you thinking of to add to your tank? Gravel as such isn't a bad substrate, given the right lighting, water column nutrients, and CO2, and the occacional root tab feeding, you can grow most plants very well in it.
IMO 5 cm / 2 inches depth isn't bad...
One problem with mixing fine and coarse gravel is that after a while, the coarse stuff ends up on the top, and the finer grade collects on the bottom.
So... before starting to change gravel, you should look at the other factors, as they will have a greater impact on the plant growth.
As far as I can see there are several options of adding substrate...
- complete teardown and re-do
- take out all fish and remove as much water as possible, then add substrate, replant as necessary, let it settle down, add water really slowly, filter a few hours, and hope things clear up before adding the fish back in
- wash the new substrate really well, remove some water from the tank, and add a part of the substrate (say 25%) to keep the disturbance limited, and repeat that after a week... until you are done