Can I make a cipher (ex: Vigenère) harder to break?
For Vigenère specifically, you can make it harder to break by increasing the size of the key and by making the key truly random.  If the key is truly random, longer than the plaintext and never reused, then Vigenère becomes equivalent to a One Time Pad.

Even without going that far, it is possible to strengthen many, though not all, cyphers by lengthening and/or randomising the key.