Yes I am gaining skill, currently at about 46. I am catching special fish, but not the ones I need. Walleye, salmon, trout, etc. LOTS of regular fish, and occasional footwear (gotta love those).
Then the reason might be your 46 skill. Good to get LOTs of regular fish but not enough to get a good quantity of the fish you need for the quests.
I am not sure if it is possible to get fishing skill on jewellery, if so, did you try increasing your skill using fishing skill jewellery ?
With up to 15 on ring and 15 fishing on bracelet, you could possibly jump up to 76 skill which could help getting more of the fish you need. I never tried it though, therefore, I am not sure whether fishing skill points can be found or imbued on jewellery pieces.
As an alternative, if you can use crabs/lobsters traps, use those and the more the better. They will help raise your fishing skill faster than with fishing (more skill checks....).