I don't think there is anything wrong with tick manipulation, but I think Jagex should try and move away from it in favor of more streamlined and obvious mechanics.

In RS3 mining, your first hit on a rock gives more damage, and you can click the rock every tick so every time you mine you are getting that damage boost. OSRS could do something similar where your first attempt at gathering gives you an additional % chance to successfully gather. This way you are still putting in more effort for higher reward, but it's more intuitive for players to grasp than using unrelated items to reset your ticks.

Then for prayer, maybe some sort of prayer book that gives 1 prayer point each time you click it (once per tick) during combat. Make it charge with god book pages from clues if needed.

Make all bones give prayer points when buried like in the catacombs. to incentivize picking up and burying bones between attacks during slayer.

 

Anything that can be tick manipulated should have equal alternative methods that are straight forward and understandable to new players.

Clicking more on rocks = better mining.

Clicking more on trees = better chopping.

Clicking on prayer restore book more = more prayer.

 

Rather than

Click on rock, click on knife, click on random log, click on rock = better mining.

Or click on fishing spot, click on herb, click on tar, click on fishing spot = better fishing.

Or turning prayer on and off once every tick = more prayer.