there were a few issues with trying to prevent the cracking of the enigma:
1. Replacing them all would have been horrendously expensive (less so for the navy since they'd only have needed one for every ship), so trying to get a 4-rotor system working would have been a long-winded process that likely would have resulted in a great deal of trouble for the Germans (until you were sure everyone had a 4-rotor machine you'd have to find a way of sending a three-rotor message, thus defeating the point and giving the British a leg up on cryptanalysis for the 4-rotor)
2. There's only a certain number of rotors available, and you will have some sets near the coast, so the British will raid them as soon as they can't read the messages any more.
3. you have to let the guy on the other end know which rotors to use and what their starting positions are, and at least a part of that message can't be in code, so that offers the British another window. for this bit, that means giving them the first half of a six (or eight) letter word, with the last three (or four) letters referring to rotor positions. The key here is that the receiver operator has to work out the missing letters, but if they can do it, so can the British.
1 - You shouldn't send out identical messages in both the 4 rotor and 3 rotor codes. Just by changing phraseology between the two you reduce the value of one as a crib to the other
2 - Having (for example) 8 rotors available being used 3 or 4 at a time greatly increase the complexity of the decrypting problem, especially if you also have the auxiliary patch panel.
3 - You use distributed setup books that change the setup on a preplanned schedule.
These books might have the daily rotor numbers, starting positions, and patch panel connections. This is written on paper that can be destroyed quickly. Each day when changing setups you destroy the page for the previous day. There can be special emergency books that would be 'one time' setups that could be used for special cases.
These are all standard procedures that are used even today