Reacting properly is all about how you distribute your focus. You can break mediums on reaction, but that takes a large amount of your focus away from other options the opponent might use (such as giving them the opportunity to go from an opener into a heavy linker)
Here's a good starting point, but remember this varries from character to character, especially in regard to heavy linkers because some are decently fast while others are ridiculously slow.:
Let lights rock (mostly)
light autos- don't try to break them on reaction. Most people can't break them on reaction easily, people who can are exceptions, not the rule. But that's not an issue. Lights don't do too much damage. If your opponent sees your are completely ignoring lights and gets too comfortable using them- that's when you can start making reads and guessing on their breaker strength.
Break medium on prediction
Mediums are reactible, but it's better to react to them when you are putting ALL your focus into reacting to mediums specifically. You can't just be ready for your opponent to do a possible linker, or a possible medium. To break mediums most reliably you should before hand say: "if the next part of the combo is a medium auto, I will break it."
The disadvantage of this, is the opponent can use this to "sneak" pretty much most other options (apart from heavy autos) by you. Particularly after an opener, if you are putting all your focus into looking for the opponent to do a medium so you can react better, this is a prime opportunity for the opponent to "sneak in" a heavy linker. This is only possible because openers can be canceled into either linkers or autos, so you are most vulnerable to this at the beginning of combos, and less vulnerable after.
If for some reason putting all your focus into breaking mediums still isn't working, you can narrow your focus distribution more. Don't just break any medium, but settle for ONE and only ONE type of their medium autodoubles. choose either "Punch mediums" or "kick mediums"- and focus completely on looking for that specific medium punch cue or medium kick cue appropriate to that auto. This means will decrease your chance the opponent will throw something your way that you can break, but you are MUCH less likely to get locked out, meaning you will still have opportunities later in the combo to try for a breaker as your opponent continues.
Break heavies on reaction
Heavy autos are really slow. Unlike mediums you don't have to set aside all your focus specifically to breaking them. After an opener, you can be on the lookout for both heavy autos, and heavy linkers, and be able to break either of these. You should actually be able to look for one type of mediums of your choice, and still be able to break any possible heavy auto.
So think of it this way:
Your total focus points to spend 100:
33: deciding you will only break one type of medium auto if you see it (med punch or med kick) "If I see jago hit me with his right elbow like that, I will break medium"
50: deciding you will break any type of medium auto if you see them. "If I see Jago hit me with either his right elbow or his a low strong kick, I will break medium"
33: Deciding you will break any type of heavy auto you if you see it
33: Deciding you will break any form of heavy linker if you see it. "If a linker hits me three times, I will break it"
Of course, it doesn't exactly work like this, but you get the point. There's a reason you see players use heavy linkers most commonly after openers. It's because opponents are putting effort into making sure no type of medium gets by, while still accounting for heavy autos, and thus it gets snuck past em'.
The fewer animations you have to look for, the better your chances. So I reccommend you start out only breaking mediums if they use the strength of medium you predict they will use- and this way you should still have enough focus to protect from heavy autos.
