So, I've been working on this more, and I think I've figured out a
good method. It requires a lot of note taking, and working in pencil
first, but it seems fine. If anybody wants to play around with it,
feel free and tell me how it works out.
As a side note, I'm calling this setting/rules mod Deep Ether; from
the old ether sailor saying "In Deep Ether", which means a situation
that can, very quickly, turn very dangerous.

Note on the Ether: It is, by some miracle, breathable, and barely
flammable. It is also exceedingly cold, with even the heat of a sun
providing the merest noticeable increase in warmth. Atmospheres of all
kind, with their ability to hold heat, are a function of gravity
condensing the Ether into gasses of all kinds. Then the planetary
processes (scientific and magical) take over, and who knows where
those can lead? The overall effect of the Ether is much like living in
a nebula - color is everywhere.

Prep an 8x10 hex map, with a sheet of paper. This represents one layer of space.
CURRENTS AND TRAVEL TIME: Currents are just about everywhere, with
strength varying across space, which effects the base travel time
across each hex. Roll 2d; 4- (W)eak Currents, 8 days/hex; 5-9,
(M)iddling Currents, 6 days/hex; 10+, (S)trong Currents, 4 days/hex.
To this travel time, add 1d days.
(Still figuring out how better FTL is going to effect travel time. I
might just leave FTL as not effecting travel time)
UP/DOWN CURRENTS: Up and Down Currents lead to different levels of
space, either one up or one down. Throw 8+ for these to be present in
the region, DM+1 for Strong Currents. If generating a region above or
below a previously generated one, throw 8+ for the corresponding type
to be present. If present, roll 1d-2 (min 1) for both. Place as you
like. Random placement can be done with a series of odd/even rolls -
the first one determines if it's present in columns 01-04, or 05-08,
the second for rows 01-05 or 06-10. This shows which quadrant of the
map to put them in, and an addition series of odd/even rolls can
determine the hex (Odd or even row/column, then which specific column,
with rows being determined by 3- and 4+ on even rows and 1-2, 3-4, and
5-6 for odd rows). Currents are marked with arrows in the hex pointing
up or down, and override all hazards and stars
HAZARDS CHECK: These are barriers to navigation, being (R)eefs -
collections of stellar debris, or (V)oids - where no currents flow.
Throw 10+ in each hex for their presence, then roll 1d for their type:
- 4- Reef 5+ Void.
VOIDS: Voids cannot be traversed. When a void is placed, check each
surrounding hex for the presence of an additional void; 10+ indicates
another void is placed in that hex. Throw 10+ for additional voids to
have a chance to generate other voids. If successful, follow the
regular rules. Voids are noted with a V in their hex. Stars cannot be
placed in voids.
REEFS: Reefs roll 1d for their Density, which indicates the number of
objects that pose a hazard to navigation. Crossing a Reef requires a
Navigation Check, and a Piloting check, with a penalty equal to the
Density. These penalties can be avoided by taking twice the penalty in
additional days of travel. Unlike planetoid belts in systems, reefs
can indeed be thick enough to see a few hundred objects with the naked
eye. When a Reef is placed, note it, and its density, in pencil as RX,
where X is the density. For Density 2+, check each surrounding hex for
a Reef of one lower density, placing one on 10+. This reef can then
check its surrounding hexes if it has Density 2+ (multiple reefs can
check the same hex). This can create entire fields and chains of
reefs, creating natural borders and pirate havens. Stars override
Reefs, but only in the hex where the star is placed. When placing
stars, note the ones that overrode reefs - these will gain a bonus to
the number of planetoid belts they possess. Once all stars are placed,
finalize all available reefs in pen.
STARS: Stars will be initially placed in pencil, or on the notepaper.
For each hex that does not have an Up/Down Current, or a void, throw
8+ for a star to be present.
STAR TYPE: There are three types of stars in Deep Ether - (D)im stars
are small and feeble, usually red or other dim colors, and barely warm
their systems. (C)ommon stars are, obviously, the most common, with
reasonable brightness and warmth, with colors that range the rainbow
(hey, I said it was fantasy... Purple stars, anybody?). (B)right stars
are massive infernos, sometimes regulating life to hide in the outer
system in the shadows of asteroids and planets.
MAGIC: Stars influence the amount of energy a caster can pull from the
ether. Roll 2d, with a DM of -2 for Dim stars, and DM+2 for Bright. On
a 2-, the star is Dead, having no ether available to replenish it, or
the atmospheres of their worlds. Mark Dead stars on the map with a - ,
and roll 1d for Drag, placing it after the mark. On a 12+, the star is
Overflowing. Mark these stars with a + on the map, and roll 1d for
Boost, placing it after the mark. Otherwise, place the star with an O
on the map, and noting the magic levels for later. 3-5, Low. 6-8,
Medium. 9-11, High.
Hexes with Dead and Overflowing stars cannot be traversed, but have an
effect on the currents surrounding them. Drag multiplies travel time
in the hexes that immediately surround Dead stars, as it calms and
eddies the currents before slowly drawing them in system. However,
Storm checks suffer DM-2, and traveling storms will dissipate within
hours of hitting the zone.
Overflowing Stars Boost travel time, dividing it by the listed amount
as they push raw ether out in powerful, chaotic, winds. Unfortunately,
they penalize Piloting checks by DM-3, and give Storm checks DM+2, in
addition to causing a storm check twice a day.

I'll cover worlds (and navigation, and storm checks) soonish, since
I'm working on the rolls building a World Sheet. However, the first
three are the same - Size, Atmo, and Hydro.