Oh man, I'm going to come right out and say it.
I actually liked Rubicon's texture set.
It's not that I approve of grey-washed and ultramuted colour schemes - I can't stand Quake I, or most Quake games, for that reason - but for me, Rubicon strikes the right kind of balance between vibrant colour and a more subdued realism that supported the scenario's story and play style well. I'm not particularly fond of their Phfor set at times, but I'll stick my neck out and say that I thought as a whole the set was better than a lot of what has been made, including M2.
(FULL DISCLOSURE: Rubicon was my first full contact with Marathon. I only got the main games later, and I seriously can't stand the Phfor set in any way except extreme darkness. A lot of more recent scenario texture sets continue to burn my eyes with their insane neonanity.)
I know a lot of people disagree with that, but, you know, whatevers. I thought there should be some divergence of opinion here.
Anyway, in regards to your scenario - do whatever supports your work. Tempus Irae seems to me to be a good example of a vibrant texture set that isn't cheesy, Goran's later work with his own textures is also impressive (to me), and if your scenario feels that way you could do worse than examine how they balance colour into their mapping. I guess it doesn't really matter how great your texture set is if you don't lay it out and shade it right in the maps? Do what feels right to you.
