I was a pretty big fishing enthusiast in FF11 and FF14, so I'll go over your points and add my own comments.
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1) The fight fishing system: I liked how the fighting fish system worked and how challenging it was most of the time, mostly while catching Ebisu fishing rod fish. The current XIV system is boring, and alike all the other (Botanist, Miner) which gets me bored after lvling Miner and Botanist to lvl fishing in almost the same way.
I wouldn't mind seeing this come back, but if they did this I think that they'd need to make the other two gatherers more interactive. There can be some counterarguments to the whole fisherman standing in one place vs botanists/miners having to run around to gather their nodes, but as it sits right now, all are equally easy to bot from testimonials I've read. I don't think fisherman should have to work harder (i.e. click more buttons) than the other two to get their items.
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2) How hard it was to get skill ups: Fishing actually needed alot of effort and work to get to 100, which was good because every game requires some challenge in order for people to actually feel proud of having it at cap when they reach it. The current system is too easy, specially if you take the leve's to level it.
On this one, I'd actually rather them keep about the same rate of xp gain as it is currently. I recently started FF11 back up since there's not a whole lot more I want to do in FF14 at the moment. I went out and fished up around 50 fish over my level and didn't see a single .1. I really would like to feel like I'm making some headway each time I go out and fish.
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3) Fishing quests: 'Inside the Belly' was the main fishing quest, where we whouldnt only need to sell fish at the AH or craft it or NPC, but actually give it to NPC's in a hope of obtaining an item that supposedly was "inside the fish belly" and whould actually give good items, such as 'Pirate's Char' and 'Brigands Chart' which mostly only Pirates droped the best multi-hit dagger in XI till the introduction of Abyssea Augmented Weapons.
I really want to see things like this come back. Gatherers in general need more content if they don't want them to feel like a "sub-class". They've mentioned there's going to be things such as treasure maps that you can obtain, but having some other content like the fish gutting would be nice. There's a fish that sells for about 500k on FF11 right now since it has a chance to give you a cape that increases your rate of skill gains while crafting. Things like this would make fishing a more desirable class to take up.
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4) Fish on the boats: I loved this part, specially when there were RMT bots fishing there and pirates showed up and kicked their butts off. Aside of kicking RMT's butts, i loved the challenge to solo Silverhook and Blackbeard as SMN for fun while having a quick fishing break to do so. Not only this, but also the possible fish caugh changed too, and we had the chance of catching 'pirate's rides only' fish.
I'd definitely love to see a boat route or two set up that was long enough to get a good stretch of fishing in. I liked the Manaclipper in FF11 because it was basically three separate boat rides and each area you could fish in produced slightly different fish. There was even an NM on one of the rides that could only be fought by fishing it up and you only had a small window of time to kill it before the boat ride ended. Things like that were pretty fun. Not to mention the pirate-only fish you had to catch to gut open for baits to get the Ebisu Rod.
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5) Rod Breaks: This was totally mean at times, but was actually good, so people couldnt just grab a weak rod and fish most of the fishes avalable in the game with it. Also made fishing more harder to lvl up, which was good because not everyone had it maxed and it was actually hard to get there. Also the contests for Lu Shangs and Ebisu were challenging and people actually aimed for those rods to actually be good at this (craft? i think it was considered a craft in XI since it was in the Crafts list).
I don't think this should really be a factor anymore since durability plays more of a part on your fishing rod nowadays.
Now, here's some thoughts on what I think could improve on the fishing system overall:
1. Fish need to have more applications than they currently do. I think they're in a pretty good spot for alchemy, but I feel that they need to have more of a presence in higher level food than they currently do. This will create more demand for different fish and more people may take up fishing. Also, things like the fish gutting from FF11 that can reward gil or a useful item rarely would create more demand for certain types of fish that are current underutilized.
2. Baits in which fish favor and fish distribution by area need to be improved on. I compiled a spreadsheet a long time ago tracking which fish favor which bait, and for most areas all the same fish respond to the same baits. Even when fishing at the sweet spot for a certain fish with favored baits, you'd still get things you weren't targeting more often than not because they liked the bait too.
What I feel needs to change is the favored baits for each fish need to be reworked first. (there's at least 6 fish right now that don't even HAVE a favored bait) After that happens, distribute the fish in each area in such a way that only a maximum of two fish per area will like the same bait. This way, it makes it a lot easier to target a specific fish. Also, with the exception of shell bugs, vendor bought bait (not lures) currently favor no fish. I don't know if this is a balance decision since these baits are intended to be used by starter fisherman and it shouldn't be as easy to single out certain fish with them or not, but I just wanted to point this out.
I think these are really the only couple things I have issues with the current fishing system in addition to the ideas of the OP I agreed with. I like gathering in general and I hope to see all of the DoL's improved on, but fishing holds a special place for me so that's why I'm writing a little more in depth about it.