The answers to your above questions are the real code of angling and a life time of experience is not enough to answer it. We can only suggest some general rules. The choice of Live bait vs Lure vs Spoons Vs Fly (You have left out Spinners, Poppers and Jigs) actually does not exist as far as fish is concerned. These are different style of fishing techniques and you can target same fish with equal success by using above mentioned techniques.
The logical conclusion theoretically should be that live bait should work best as all other artificial baits are but imitation of live bait but many a time you will find that artificial lure produce much better result than the live bait.
There are some established patterns and for start you should stick to them. I am listing below some of the fishes and established method of Target them ,
1- Talapia, Khawli and Mirgal Small J-Hooks with earth worm/ Atta / Larva etc. Place your hooks 4-6 inches above the bottom.
Medium Round-Hooks With Atta and place your hooks on bottom.
3- Catla and Silver carp
Dont even think of targeting it .
Spoon and Spinners work best but you can use live baiting for it Also. The conventional method is bolt rig with a 6-0 to 8-0 size hook and rotten fish as bait.
You can target them by almost all the methods but Spinners and Soft bait (Frogs) works best. You can live bait a frog around the edges of weed etc.
They are also known to prefer crabs but live baiting of crabs is very complicated.
Almost all north mahseer are caught on Spoons, lures, spinners or softies but In southern parts this fish is caught on Ragi or live baiting. You can live bait for them with Chilwa or Crab. Some time good mahseer is also caught on Atta (Yellow Colored) as bait.
Small spinners or Flies are the most successful methods but the purist amongst the angler community will only accept flies.
There are many more fishes (I have not even started salt water) and many more techniques to target the above mentioned species but as I said these are the general rules.
In case you want to target any specific fish, feel free to ask.