Do they? The only deleted scenes I can think of that actually improve the prequels are the Padme scenes from RotS. Giving her more agency is a good thing, but they don’t go anywhere. Maybe there could be more deleted scenes which give the Delegation of 2000 more purpose that we just haven’t seen, but I kind of doubt that. Padme was cut down because Natalie Portman was asking for more money than George wanted to give her, so I wouldn’t be surprised if most of this plotline went unfilmed.
Most of the other deleted scenes were cut for a reason. TPM and AotC are far better off without any of the deleted scenes (that we know about I suppose), and that’s including the ones that were re-inserted on re-releases. I feel like re-inserting deleted scenes would just be bloat.