Even though I like most of your suggested changes regarding the fishing-system, I'm not fully on board with adding four new items just for fishing. I would rather see items already in the game getting aditional features instead of adding new ones. For example you could maybe replace worms and bread crumbs with different seeds and netherbeetles with netherwarts and nightstalkers with chaurusfruits.
That's a good point. Right now there isn't much of a point behind getting say beetroot when there's wheat. Adding their seeds as bait would solve this issue. On the other hand, bugs are a common bait irl and worms would give a use for dirt. I'll make a poll to see what people think.
It is no longer possible. The bobber must be in the water for more than 5 seconds for a chance of treasure (which only occurs 15% of the time now).
I fully approve of this idea. I would add that certain water blocks only hold a certain amount of treasure items you can obtain by fishing there, so you would have to move around and not sit in one place to get loot. It would completely finish off AFK fish farms, as well as add a bit more realism (eventually a certain area would no longer have anything useful, right?).
This is also a hard decision, but while it does make more sense this might be annoying to those who want to fish by their base. As McNubberson points on servers fishing would become quite difficult.
Good point, I'm changing that now.
Recap. Fish mobs should increase fishing rate. See my bait suggestions. Rods aren't totally useless, I use them all the time. It's the way I, and many many of my other friends like to fish. It's a great way to sit around and just BS about other things than just minecraft. Just like real life! Also just like real life, when we catch something "spectacular," we trade for it, it ups our economy. It also drives some server economies.
While some baits repelling fish and others not would be interesting, Minecraft doesn't seem to have a preference over fishes. If I catch a salmon I wouldn't really care that it wasn't cod- they both serve the same purpose. If there was more variety between fishes this would be a very interesting system, but as it stands I don't see how this would work for the average player. Since each fish species lives in a different ocean biome, this can still play out to a limited extent with villager trading. For example, a taiga villager requests a tropical fish, so you venture to a warm ocean and fish for one.
Remember the chances of getting treasures are per person, so even everyone was fishing in the same pond they would still all have an equal chance of getting something (not very realistic, but gameplay is more important). Now that I'm thinking about it, fish mobs will need to be more common. Every lake or river should have them.
As for trollers attacking the fish coming to the bobber, I haven't thought of this before. Fish are faster and the distance is quite short, but I can see someone trolling. If that happens remember that you'd be close to the troll and they'd have wade through the water, so just attack them. This could be fixed if the fish had more health, but that might be too unrealistic.
I suppose you could get a friend to sit by the bobber and share the fish. That way you keep your bait. But your rod would be taking damage as would your friend's sword (which would be better spent against mobs). And you wouldn't get an XP out of it.