Your suggestions seem perfectly viable, but I was thinking that the impact of different factions could be a little more diverse. For example, the Initiates could 'upgrade' your Artificers' Facilities and Artilect Posts, but the Shapers might provide free biosculpted housing for your Freeborn and new crop species to grow, while the Collective might create gardens and improve water-reclamation, or the KotSF would upgrade your power stations and mining facilities. As in, the effects of a given faction wouldn't be limited to just the one structure type, but actually pervade the settlement as a whole.I like the idea of all-in-one sentry station with various upgrades.
Although I like the idea of being upgrade temples with their own uber point defenses in case you really have a fight over one.
I mean, the thing that always struck as me odd in the original Majesty was that you could get these bright, cheerful, colourful buildings like the royal gardens and straw-thatched cottages in the same settlement with temples to Fervus and Krypta. They didn't match at all!
Ooh- a few further things.
Music
This is a subject on which I'm really woefully ignorant, but for what little it's worth, I would make two main suggestions:
1. Have a strong basic theme. Majesty had this, and though it showed up very little during actual play- which is a pity, because it's the best music in the game- It really summed up what the game was about better than a thousand words on the subject, and helped to give a sense of structure to the other pieces.
For what it's worth, I reckon there ought to be a single piece of music that really communicates the overall 'feel' of the game to the player- and you can then produce variant riffs on that theme to cover different situations/contexts/eventualities. So, just a thought.
2. It might be possible to vary the music depending on what the curently selected character is doing, and/or what faction they belong to, and/or what's generally happening on the screen at the time. I think this kind of context-sensitivity might encourage or reward the player for following the lives of individual characters.
For examples of 'tone', I'm mainly pulling music from Bear Mcreary's work on BSG and the work of Yoko Kanno because... I'm clearly a dangerously obsessive fanboy. ...But also because they've probably produced the best SF soundtracks in recent memory.
That said, although I think these could be useful as a source of inspiration, these are mostly a tad too too 'heavy' for a game in the relatively light-hearted spirit of Majesty, and their overall 'mood' might need to be leavened considerably? Anyways. Yoko Kanno is awesome.
Large Scale Combat- Destiny.
Stealth/Deceit/Subterfuge- Gina Escapes.
Manufacture- possibly Fingers?
Peaceful- We're the Great. For an exceptionally large, well-developed and content settlement, maybe Some Other Time. Yes, there should be peaceful interludes in a Sim-style game. (How else are your characters going to shop, rest, hold conversations or have any sort of personal lives without looking like oblivious morons?)
The Initiates- Flesh and Bone, possible combined with some of that eerie-ass monolith singing from 2001.
The Spacers- Something Dark is Coming (actually rather meditative and beautiful, IMHO.)
The Collective- Something halfway between Pegasus and Monochrome, maybe?
The Shapers- Surf, I think.
The Jovians- original theme to Ghost in the Shell. Haunting, alien, cyborg wierdness. Perfect!
The Krech- maybe Cats on Mars?
...Again, these are mostly a bit 'heavier' than is really suitable for a Majesty-style sequel (BSG, after all, is definitely darker than you'd want.) I reckon the trick here- as with the game in general- is to inject a sense of levity and playfulness that doesn't undermine the integrity of the world.
Voicelines
There are potential complications here. If you abandon the idea of One Character One Class- which is basically neccesary in order to have heroes with multiple lifepaths or even basic 'class upgrades'- then you need to keep the same basic voice for different voicelines.
The brute-force approach, which is probably most practical, is to have, say, a dozen different basic voices, and have each of those speak the voicelines for every possible class/lifepath (possibly with some minor variations.) Then, if you have a character who's a Freeborn/Physician/Artificer (Gaius Baltar, perhaps?) there's a random chance of him/her speaking a suitable voiceline from a given lifepath during a given situation.
It's possible that certain lifepaths wouldn't have any dedicated voicelines for a particular activity- e.g, an Artificer or Physician probably wouldn't have any witty catchphrases concerned with combat- in which case, the character defaults to the voicelines available from other lifepaths.
The non-brute-force approach is to use voice synthesis technology, but the results generally aren't great. Maybe in another ten years...
Other Possible Inspirations
Basically, imagine that you took Crusader Kings, set it in space, gave it a sense of humour, and focused primarily on individual settlements rather than the inter-kingdom map. ...That's sort of my 'pitch' here.
Fable 2, naturally the Sims, maybe the Citybuilder series, and perhaps closer to home, Deadlock, Hinterland or Depths of Peril might well be worth looking at. Or the original Stronghold.
From an aesthetic perspective, Myst, Riven and their sequels could actually be very similar to the overall 'look and feel' between the different factions, and very similar to the Dune universe- You have native tribes and alien species, a mixture of arcane technology, stately architecture and organic biosculpture, plus commentaries on ecology, family dynasty and the use and abuse of power. Well worth a look.