Given the origin of soulflayers and lamiae (which may be a spoiler for you so I won't go into detail), I don't see them adding these to "monster rearing". Even other beastmen could arguably have "souls" (that goblin kid in Jeuno who tried to unite humans and goblins), and to say you are going to raise one in a garden could be seen as cruel.
There are still some profitable things out there, namely Ebisu rod fish, but for example, people are also now farming hmps with chocobo digging. You could argue that there are faster ways to make gil, but I can see why they wanted to use a limit so that it doesn't get out of control.
Salmon can be fished in the stream right outside Sandy; it will yield either salmon or trout, so it's not that hard to fish up a stack in 10 minutes. And the salmon croute recipe yields 1-4 croute per synth, and the NPC will only let you turn in 12, anyway, so this shouldn't have been an issue. As for tuna, I get 0-2 a day from my net in mog garden on each character. My mules are overflowing with tuna for when I actually bother to sit down and make sushi. This really shouldn't be an issue either.
I don't get what you're saying here. Obviously you are skilling by playing the arrow game. Is the rate of skilling not fast enough for you? With the rings, the synth belt, and especially the food made specifically for skilling fishing, this craft was by far the easiest to level.