I'd suggest that the problems that are being talked about here are more a sign of teething troubles than an innate problem with the game, though I agree that there needs to be a much overhauled space/overland view - Just gimme a full map view of the whole L5/current region overmap like GH did with the world view and it would be simple; just look to find the spinner you want, travel there. I'd say this is one of the worst points of GH2 right now.
However I do believe that the game has the potential to incorporate other planets (effectively separate atlases via "shuttle to Venus/Mars/Luna/Earth") as well as spinners, at which point you could comfortably fit GH 1 into GH 2 with room to spare. More factions, multi-factional membership (why can't I be a crooked cop also working in the Red Mask Raiders? Who's to know?), more areas and a better overmap will all come, this is simply a content issue, and this will be fixed in time.
On the other hand, with the comments about empty cities - I think the problem is, beyond there simply being not much content to put in there at the moment (and I remind everyone with the open nature of the games Series files, they are welcome to populate the map with many little tweaks and sub-plots if they wish) that they are populated, it's just less visible than it was in GH.
Take your starting town in GH - How many people lived there that you saw? Twenty maybe? Thirty at a stretch? It's been awhile, but it's not that many. What about Snake Lake, total?
Your average spinner has a higher population than most of the cities, and because it shares its space with an SF: ~2 area around and in the spinner, there's actually a lot more space involved (in both senses) than there was in GH, each spinner is basically its own self-contained overmap. But its population is viewed piecemeal, twenty in one building, ten in another, not walking around from place to place, everyone showing up everywhere.
Now there are three paths to alleviate the problem, and they're both reasonably doable in the engine, as far as I can tell (though a codemonkey might say otherwise).
1: Make Patrols and other "non-hiding" mecha visible on the "overland" spinner maps.
They're not trying to hide, so show the leader's mecha flying around on patrol, let them be talkable-to, and leave them out there until their time for patrolling is done, not vanish home when you talk to them. Ideally they should have a fairly high chance of getting involved with any nearby missions you have, though whose side they're on depends on your standing with them - it could easily turn into a three side free for all.
This opens up other Civvie mecha - A taxi, for example, that your character can talk to the cabbie (cabbies are awesome for gossip), and even pay for a ride if they don't have a mecha. Or someone just driving to work (this would potentially require A-B pathing, or the person just doesn't really want to go to work....). Or a spacebus travelling into the station on a periodic basis (a "mission" given every X hours?).
Mecha going about their business would transform the lonely overland.
2: Neighourhoods.
You can currently park right outside Athena Mall and go shopping. Why not enforce a neighbourhood region for each of the given sections of the spinner (I'm talking about a large, outdoor PF: 0 area, where major buildings and minor buildings exist along with NPCs hanging around outside).
Want to go to Hovel Manor? You'll have to sneak past the rubbish dump full of respawning rats, the street punk gang spraying graffiti on the local corner shop (a small store with a simple selection of foodstuffs and every day disposables/goods that is a standard part of the area), before reaching the door to Hovel Manor, where entering will take you to the existing area just as going in your mecha would now.
This would give a much better feeling of scale. You can even have neighbouring important buildings in the same neighbourhood (L5 Law academy might be near to the courthouse), grouped by neighbourhood type with the population and incidental buildings (incidental in this case would be any minor building, such as somebody's home, or a cornershop, or the aforementioned rubbish dump "building") showing up as per the type; meanwhile keeping the non-incidental buildings separate as empty "squares" of building with an entryway (much like an elevator, except larger) will keep the number of NPCs running around the map low and manageable.
3: Handling Extras:
There are eighteen million people in Maquise spinner, why keep it restricted to show only a few dozen of them? And why do they stay in the same area?
Tier 1 of Extras can be handled like named "monsters". They spawn in an area, they wander around for awhile, they periodically leave the area and you either never see them again, or they show up in another area of town. They are red shirts, you might chat to a red shirt one time, but they won't show up every episode, they are never involved in the main plot (other than to die to the monster of the week), and the main character never forms lasting friendships with them. They don't even have cell phones. Luddites.
Tier 2 of Extras should mainly be handled as NPCs are now - They spawn on the opening of a map. You only need a few of them, since most of the filler population can be handled by Red Shirts. These Bounty Hunters/Soldiers/Pilots/Cops will leave to go on Patrol, or get their mecha serviced, or hunt a perp, then when they return, either go to their primary hang out, or move to another one (yes, this will cause a lot more use for the "where are you?" phone feature). These are mauve shirts, and if they are killed (on patrols or in an accidental fire) then ideally new mauve shirts should be cycled in, to keep the total Mauve shirt population at a constant.
Mauve shirts will give out a lot of the simple missions or help the player, but rarely would one expect them to form any sort of relationship with the player beyond minor Friend/Enemy status.
Tier 3 of Exras are the important NPCs - Vannis Abdiel, your family, Gordon Valeus, Shopkeepers, Trainers, Teachers, anyone whose presence in an area is reliable, whose presence in the game is vital and consistent, or who is generally someone important to the player character or to the game world/plot in general. There should be a very limited number of these yellow shirts, but again; nature abhors a vacuum, either yellow-shirts have plot-armour and only plot can kill them, or whenever a yellow shirt dies, they are replaced by a new yellow shirt that spawns into their original spot:
- Hi! I'm new to the area. There was an empty store space here, I've decided to take it over.
- I have been selected to lead the silver knights. We will not forget your hand in this Rocket Star!
- It was a terrible tragedy what happened to Matthias, I only hope I can lead us through these troubled times without him.
- Greetings, my previous ambassador experienced an untimely accidental death, I am his replacement.
Generally speaking, a show has more characters by the end than it does in the beginning, which doesn't much work if there's a slowly dwindling pot of NPCs thanks to some lucky/planned pilot kills, or the fact you took camraderie and just so happened to lose every single NPC friend in the game down in the Cayley Core one after another. Secondly this keeps the population of the spinner moving - You might encounter a Yellow Shirt cavalier spawning on a few spinners, you may help, or compete with them, on some missions (you may do both, as the cavalier will not necessarily engage in missions against the same side).