1. Fantasy is easiest. 2. Fantasy is most common. 3. Your examples are typically fantasy ones: monsters, encumbrance.
I think doing fantasy first is a very good thing. I see HUNDREDS of generic free systems and, well, they're normally not very interesting because they do not have a killer mechanic that really feels like you're playing a genre. Some generic system allow you to pick your own attributes and skills and then give you bolt on mechanics for space combat, doing net runs, dealing with post apocalyptic weather and so on. If you're specifying attributes, both primary and secondary - which you probably ought to to keep the application simple to use - then you are likely to be learning toward one genre or another.
I know this is veeeerrrrryy early days but that was just a feeling I got. I get feelings, you know.
Hex sheets can still work, (i'm not a fan of them, but) they're just obviously not to scale. Another thought for hex sheets is to have one FTL sheet and one close combat hex sheet. If two ships move into the same hex, they're considered in the close combat sheet.
Another option is to have a table and measure things off for distances like most wargames.
For an RPG however I've always just kept track of the distance and relative positions in my head. When my players need to know where things are, I draw the important objects on a little white board and then write the distances between them. An iPad with a drawing program would work similarly
In the end there are dozens of ways to handle distances and I think thats where the modules come in.
As for computers, I've got a few mechanics for computers and viruses that I've been working on that don't involve visualizing (good for modern games) the net that are mostly system neutral. They would work for most attempts to hack a starship too.
I was thinking about how to scale different stat blocks. If you say a monster should have high strength and claws, you want to have that defined with a number that will give the GM using your system some idea of how high and how nasty those claws are. The problem is, when adjusting the scale of that monster, if the reference number is a low one, and you scale over it, you loose a lot of granularity. However if you start with a high reference number (say 100 instead of 10 for strength) you can easily scale down. For most purposes 100 is a good upper limit for human abilities but it might be good to start even higher (say 1000) in case someone submits a mechanic that could use that kind of granularity. I don't know why you'd want to but someone might.
Hex sheets can work, but you're trying to run an infinite play area on a finite map which introduces inherent constrictions, although they can be a lot of fun.
I agree with the whiteboard idea, premade maps are good for large geographical distances like fantasy kingdoms, but on a more local level you run into problems with the group seeing areas of the map that they shouldn't, unless you physically cut up the map. Another thought - maybe give every account a simple javascript whiteboard? Some people don't like computers of any sort at the table, but for those who do it might be a handy and easy to add facility.
You've hit on another problem with designing effective generics, as well as a reason why a death spiral is difficult to implement, larger or smaller creatures would use a different scale of damage vs combat effectiveness. It's a pretty straightforward to create a system that just works for humans, but to properly encompass battlemech sized creatures in a balanced manner in the same system is a whole other kettle of fish. One possible solution is not to make stats linearly advantageous after a certain point, for example a a droid with a strength of 14 would have effectively double the strength of a man with the maximum strength of 10, not 40% higher, in terms of game effects.
Of course you can avoid all that with non hit point systems, but I likes me some hit points.
That looks good, I'd be a little wary of stepping up to a scale ten times bigger though. Give it a blast and see what happens sure, as I recall Rifts had a similar idea with their megadamage system.
Megadamage was different in that it was a one way street. SDC weapons could not effect MDC structures and very early on, it was written that any MDC weapon would destroy any SDC structure. Later it was backed off a little, although functionally it was still true.
I'm not talking HP here though and this is still a linear system, it's just testing against the two most significant digits but can mostly go on forever.