So, I don't know what is causing it, but loading up SKSE ( No mods installed except for Sky UI and the most recent version of Phinix ENB) takes about 1-2 minutes, and I can't really pinpoint a cause or give any more info, I hope someone here would know, as it is kind of a pain to have to wait so long to play the game.

Could be the ENB especially if you have HD DLC texture pack and or any other texture packs.

I'll have to try and remove the ENB and see if that changes anything, would using the injector version as opposed to the wrapper version help at all?

I have no idea since I can not really run ENB on my notebook.

Ah well, i'll try it and see, hopefully it makes a difference.

EDIT: Made no difference, went down to no ENB and still super long load times, around 3 minutes after timing it, I am at a loss here, I just don't know what to do.

Not sure if this would help, but you could try moving some of your old saves to a different folder - pure speculation here, but I'm guessing SKSE reads your save files on load - if there's a lot, it might cause lag.

I get the same thing as the OP. In earlier versions of SKSE it was fine, and I had the same amount of mods. Now, though, it takes a few minutes to pop up the little box in the corner and begin loading the game. I don't use an ENB.

In regards to saves, I start new sessions with only one save in there. The normal one and the skse file. When I can't be bothered playing anymore, or my game crashes, or locks up (whichever comes first), I move the accumulated saves to another folder (then eventually to an external hard drive), and always make a new save, never overwriting. I don't think it's anything to do with saves, though.

Somewhere along the line something changed with SKSE - maybe as there are more updates and the program gets better, does more, whatever, it just takes longer to load. Dunno, just guessing.

But, yes, I have the same problem.

For me, that happens now and then, but (apparently) randomly. Sometimes Skyrim starts up right away, sometimes I get the Uncapper flash screen, and then nothing happens for about 30 seconds or a minute (not more, yet).
As Skyrim runs just fine after that, even if it takes its time at the start, I just live with it.

Yeah this happens to me occasionally. I think it's more to do with the OS putting Skyrim in a "waiting line" while it shuffles through other processes.