After a couple of months of official live-play, EA and beta, one of the things that continues to 'break' the flow of gameplay most drastically are the cooldowns. Specifically the companion cooldowns, but to some extent also the breeding cooldowns (or rather expecting and nesting cooldowns) and even the cooldown on Tiny and Bigs' accepted payment offer.
In short my suggestion is to change their cooldowns to work similarly to the Mole Market refresh and claiming a free item. Meaning that regardless of when you perform an action (or in case of farming, refresh te page), the counter to do something started at the hour on the dot.
For example, playing with companions with a 1 hour cooldown. At 0.00 (midnight) the button becomes clickable. But regardless of whether I play with them at 0.01 or 0.59, at 1.00 the button becomes clickable again. For 2 hour cooldown companions this would obviously be at 0.00, 2.00, 4.00 etc.
Using Nana is only really worth it if you have expensive, high rarity companions like those exclusive to moonstones or the kickstarter companions, ánd only if they reward pebbles. When you have a large amount of common companions and/or companions that award stamina, experience or items, you often end up losing out when using Nana. This in and of itself isn't an issue. The issue arises that when you decide to manually play with each companion, their cooldown doesn't reset at the same time. Cycling through them at different speeds often means I have to wait a couple of seconds or sometimes even minutes if I got distracted for a moment during my previous cycle, before I can play with the next companion. As I said, this completely breaks the flow of gameplay, makes the process of bonding with companions take longer and longer on each cycle, and ends up being pretty frustrating and not fun.
And while for the more common companions with the shorter cooldowns generally this lag in the cycle is reset when you go to sleep, when it comes to the rarer companions and breeding and nesting, the delay just continues to grow. Specifically for the breeding cooldowns and nesting I would like to see a day countdown rather than one down to the very second you bred them. Basically if I breed my Lupin today, regardless at what time I bred him, the cooldown ticks down to 7 days at midnight, to 6 at the midnight after etc. Same for nesting. Regardless of what time I put the wolves on the nest, the next day at midnight they can be born.
I feel that this makes it a lot less punishing if you happen to forget for a few minutes or hours, or if some RL obligation stops you from being online the very second the cooldown is up, potentially messing up and slowing down your entire schedule.
Same goes for tiny and bigs. Especially now that the amount of items they can potentially ask for has been expanded, having the cooldown start the moment I open the page rather than on the hour, is pretty frustrating if they keep asking for food I cannot make because I don't have the right ingredients.
So in short, rather than make the cooldowns specific to the very moment I clicked a button, make them dependent on the Lorwolf clock, and anywhere within the timeframe of their 'cooldown' period (whether it be 1 hour, 2 hour, 6 hours or 1 day) I can perform the action, and it will reset again at the lorwolf clock, and not exactly x hours after I pushed the button.
As a side note, another ideal change I'd like to see to the companion cooldowns is that companions can still be removed or swapped out even when they can't be played with. But IIRC I already made a rather elaborate suggestion about that elsewhere. Let's just say here that I hope that perhaps a change like this doesn't remove the (technical) possibility to remove companions or maybe even opens up an avenue to make it easier to code.