Li Shenron
Legend
Solution is to make the dragons like you want and not change it. It's the very same as if you were given rules. Unless the players are going and looking the dragons up and metagaming, and if you allow that then let the players into your design process. otherwise I don't see the problem if all red dragons are the same casting the same spells. Either you are given rules or make them up and keep with a consistent ruling nothing should matter! Happy gaming!
The problem with making them up, is that you're on your own trying to figure out how the changes affected the encounter difficulty. Which I think should be the purpose of the books... Sure if I just give a dragon one spell per encounter, it's not going to have much of an effect, and it's already a small interesting change.
But for example, if I have CR 10 dragon and I want it to be more tactical and versatile, so I give it a few levels of Wizard. What is the resulting CR (or XP)? Maybe there's a minimum spellcasting level (2 or 3) which doesn't even affect CR/XP in practice. But more levels will have an effect for sure.
This is the kind of job that I want the MM or DMG to do for me. At least if the baseline of most MM monsters are as low-complexity as they are now.
According to Morrus in this thread, innate spellcasting for dragons is presented as an option in the MM if you don't want to use the monsters-with-class-levels rules.
So there are going to be monsters-with-class-levels rules in the DMG? If this is confirmed, then great news!