I think I will agree Factorio is intended to be somewhat organic. There are a few random elements in play for each world -- resource placement, the growth of biters (see the World Generation for default interval windows).
I've had good success with a basic belt system supplemented by robots for balance (0.17), getting a number of worlds to rocket/space science..
1) Early game, start a basic red+green science with stone furnaces.
2) have scouted enough for a good wide belt area, leave single sideways belts to preallocate a belt area (let's call it south to north).
3) Develop science up on one side (say East), and mostly circuits on the other side of the belt (west), initially with underground belts under a few cliffs for now. Send science DOWN the belt on sides of belts to save time and seamlessly be inserted into a science matrix. As soon as useful science is up, set up one assembler making the new thing and putting the output into a box.
4) further back past the beginning of the belt a number of screens, set up the refinery operations as its own octopus, with the belt "backing up" toward it steel, iron, copper (For batteries, cliff explosives, ammo, etc), and sending up acid, lubricant, plastic, batteries, cubes, etc, into the belt.
5) mining and processing further out away from the main base deliver in more belt lanes, keeping away from the main factory area (deliver by train, belt, etc). (Note iron plates have stacks of 100 vs ores 50, so that saves more space in trains/boxes)
6) once robots are mass produced, replace all the "one off" boxes with passive (red) chests, and use them to keep critical assemblers working at full speed. Also find where you have effectively stopped lines and have filter inserters put the excess into passive (red) chests from the very end of lines, or front-splillover with splitters (output priority=mainline, with excess to passive box). For example pretty much all science pack source materials are useful to have in the logistics network!
https://wiki.factorio.com/Science_pack
More high level:
Keep refining away from the manufacturing plant. Set aside a large area for oil refining away from both plant and furnaces (ideally nearish to water and coal).
I visualise the belt as the trunk of a tree and one side's large branches each make one science pack. To simplify the plan, I start by putting down an assembler with the pack, then look at the requirements, then plunk down several more blank assemblers a few squares away (not worrying about connections at all at this point!), and program THEM with the requirements. I look at THOSE requirements, then repeat. It should generally come down to belt-delivered items or things we already have (blue science's oil octopus notwithstanding). I then set up all the belts to get a trickle of ONE of each assembler to get all the components running (with space to increase to dozens at each step), but this will ensure the recipe is right and I have all the pipes and belts set up. I also double-check the grid power level before scaling up.
With Factorio don't be afraid to not understand as you build. See my above where you wade through all the science dependencies and try to get the things the science calls for, then try to scale it up. Learn! More bottlenecks will then appear as supply/demand on your mines/assemblers works itself out. Power browns out so inserters can't grab. Bolster everything up, and in the meantime, labs have researched all the way to the end of the next sciencecolour! Open the next science; repeat!
P.S. As blue science is the focus here, note that you need 2x as many blue assemblers as all the others to get a steady flow (see the link above) : 5:6:5:12:7:7