I really dont get it. Cool down to me, means stop training troops for 2 hours when the Pirate Catcher goes offline. I apreciate the 26 hour cycle so people in different timezones get a chance to fund etc, but why does it need to stop at all. I cant think of a single reason. Why not have it on a 22 hour cycle, which means it gets funded more often and people can keep playing the game the way the like to play it. There is a huge difference between 45% and 0% on the pirate catcher, thus why I and I assume others stop playing for this period. Same applies to the other perks also.
It is for the benefit of people like me who play 24/7. Those two hours allow me to sleep for 1 hour and 45 mins, take a quick shower and pat my two young kids on the head as I rush back to fund it for my next 22 hour marathon raiding session All kidding aside, I also never understood the purpose of the cool down in certain guild perks, especially those offensive in nature. There might be a slight valid argument for the defensive guild perks, but even that argument would be weak at best.
Think you hit it on the head about the timing. Putting a 2 hour cooldown in a 26 hour total cycle allows for the perk timing to be offset by 2 hours everyday. This means the time of funding rotates every 12 days and gives the multinational guilds a chance to fund at a time convenient for them (and not, say, 4:19 AM). I see your point though - players usually take breaks around the cooldown time.
I guess they did this to make the game more challenging and way ahead in the future that people can somehow needed to wait and take a break.
I think it also forces players to adapt. The army you send with a L3 Blacksmith may not be the best one to send with a blacksmith in cooldown. Still, it's more of an annoyance, especially since the PC is now such a huge time reducer. And my MAJOR problem with this.. Stuff which is begin during cooldown doesn't get the bonus when it's funded, so I say move the PC and Observatory to a nonstop 22 or 26 hour cycle. Defensive buildings, I can live with a cooldown.
In theory it was probably a good idea, but in action its pretty terrible. I am all for the 22 or 26 hour without a cool down to move it around timezones. And like @Kelani mentioned earlier, for me at least, without having the lvl3 blacksmith up, I would choose a much different army.
All of our perks are up for funding at the exact same time. As much as I hate the cooldown time at least it offsets what time of day they are up for funding so it's not always the same people day after day funding them all.
I like the cycle and it also means you can hit bases that are not perked 24/7 2 hour window. Works for me as said above time zone thingamejig.