I said realistically style rather than a Role Playing because in the latter it's quite usual limit your char to certain quests or factions. However, I want to do Everything in one long play through, but but but, make it flow in a logical sequence that could feel real.

For example, one thing I have worked out is how to do Dark Brotherhood without being deliberately evil. It goes like this. Your innocent char get a couple of assassin attacks automatically, so when you hear the rumour about Arventus in Windhelm, you get involved only with the intent of contacting a DB agent, hoping to perhaps payoff the contract on your head or find out who took it out. But no one shows up! So you go to Riften hoping to intercept the DB there at the Orphanage, and only then come to realise that killing evil Grelod is the only way to get their attention. Then it all takes on its own momentum with Astrid abducting you etc. but still your char is convincing themselves that the initial kills they perform is part of the cover to infiltrate the DB. Soon you char begins to enjoy doing the assassinations and belatedly realises they have become as bad as the DB themselves and then their indoctrination is complete .

Sorry its a bit verbose, but that is how I get from heroic dragon killing village saving good guy to evil psycho.

My question remains...... How, in that kind of realistic story kinda way, can you sweep in the other factions and make it flow from one to the next so eventually doing the whole of the questlines. I mean like no one is gonna just wake up one random morning and say, oooooh today I feel like getting right into the thieves guild and getting promoted to top thief. There needs to be. Rationale, at least for me.

Any ideas even on just one or two starts in like maybe companions and the college at WH. I don't mind what order I do the quests as long as it's got logical flow..........

It doesn't necessarily have to be a purely "logical" flow. Look at your own personal life... was it really a "logical" flow?

People stumble into stuff accidentally all the time. They stumble into relationships, into careers, and into places that they never intended to visit when they set out on their journeys.

As long as you find a reasonable rationale to start the journey, then it's up to you to construct a reason to continue. Killing Grelod can be justified in any number of ways (after all, she's never going to let them be adopted and happens to be cruel). As for what happens after that, you could decide that you like killing, or that you want to learn the ways of the Brotherhood as it might be useful in the larger fight of the Civil War or the battle against Alduin, or maybe you just lust after increased power and influence, or maybe your character finds they have a taste for blood, or maybe they just like getting paid. You might even justify it on the basis of your personal "honor" in that you've committed to joining the Brotherhood. Even thieves and assassins can have a code of honor.

An easy way to sweep it together is to get to the point where you realize that your main battle is against Alduin. Since Alduin signifies the end of everything, then you can justify pretty much doing anything as long as it helps in saving the world. What does personal honor, preference and morals mean in the face of the extinction of all life? There might be people that would rather see the world burn than go against their personal morals, however would it be wrong to sacrifice those morals for the greater good?

Outside of a handful of priests, how many people in Skyrim would really prefer that you not seek out every potential source of power in order to defeat Alduin no matter how many innocents had to be sacrificed? And given that most of the Daedra are not really good, a lot of those priests are on pretty shaky moral ground.

Anyway, good luck with your story.