Now, I'm kind've sure about what may be causing this issue.. but I'm not 100% here.

For some reason lately Skyrim's acting like Oblivion and Fallout 3 did after massive hundreds of hours where put into them. Whenever you hit the wait/sleep button it takes literally 2 minutes before it even STARTS.

You basically have to keep mashing A for the game to recognize what it's supposed to do.. lol.

Again I might be the cause of this IDK, cause back in F3 and TES4 I never kept my saves on a USB, always saved to the HDD. (Which overtime still takes long to Save/Sleep/Wait).

I run Skyrim off the HDD (Installed) and my saves off a USB (I have seperate characters). And in the beginning everything was running great, even better then before. Places would load quicker, didn't get frame stutters or lag..

I'm thinking I might have to switch all my saves back to the HDD?

There is a delay, for sure, but I can't say I've waited 2 minutes. Thirty seconds to a minute tops.

It's pretty normal. The game is processing and updating a LOT of info during sleep/wait - AI updates, script updates, weather/time updates, etc before it actually starts counting down. So I wouldn't be surprised if it's longer the more you've played a character.

Is the game autosaving on wait/sleep? This might be what is causing your problem. I do find the wait/sleep a little slow to start, but it doesn't take any more than 5-10 seconds to start (at least for me anyway). Saving to the USB tends to be slower than saving to the HDD. I used to save onto the USB but found the game runs a bit faster if you save them to the HDD.

On a side note, I did find something interesting that has sped up my game noticeably... I installed my game to the HDD and also use the HDD to write my savegames onto. Then, I moved the patch 1.4 file onto a USB. This seems to make the game run quicker. This is especially noticable when you first load Skyrim. When the patch was on the HDD, I found the game took longer to display the 'Press Start' than if you have the patch on a USB. I'm not sure why this makes the game run faster, but it could be down to the fact that data can be loaded from both the USB and HDD at the same time, whereas if they are all on the HDD, then files are all loaded sequentially and end up blocking each other.