Right, since some of the bonuses will play a pretty big part in some of the gamplay areas of the mod, I should probably outline the basic differences on what faction you choose has.
Brotherhood of Steel - The Brotherhood will obviously have the appearance of being high tech and doing stuff for the good of the people blah blah blah, but really the plus you will get from them is the free power armour training. The mod is going to include new wearable items and some of them may be pretty heavy duty, close to power armour stats if not higher, so you will need this skill, if you already have it through another source (such as doing the vanilla BoS quests) then no big deal. Another bonus BoS has is the range of upgrades for the base later in the mod, this is more in the form of defences and amount of bonus rooms that can be unlocked by the more advanced skills of the BoS engineers, but also in the speed the rooms are opened, usually it could be an ingame week or more before a faction opens up new areas of the base but with BoS it takes days. With the bonus areas for BoS you will find weapons and armour usually associated with them.
Enclave - Theyre not in New Vegas much at all, I have only actually came across a downed vertibird which I presumed was Enclave owned at some point in time. But I like them so I have decided to make them a faction in the mod, who, wether you choose them or not, will play a part in the mod. Their bonuses also include power armour training and high tech stuff same as BoS but more along their own tech and appearances, the speed they rebuild the facility is quickest of all factions because of their ways of 'motovating' people.
NCR - Theyre closest in appearance and acts as the current military in real world so I am going to try and make the appearance of the facility as close to a normal military base as I can with the current models in vanilla NV. Their bonuses will hardly be noticable till later in the mod, even then it will only appeal to those who are interested in the optional world for building your own colony on another world (I will explain that in a separate post later today).
Raiders - The raiders are tricky as you will choose the appearance of the base past the entrance because they wont know about it, the raider look wont be an option, sorry if anyone likes it. Reason for this being that it doesnt exactly fit the idea of Area 51, its too tribal and savage to have high tech stuff. There will be no bonus other than being able to redecorate any time you wish, which if you like Goa'uld or Alteran designs, might be a very good bonus.... its early yet for saying this really but if you change design make sure you remove all items and companions from the base if you expect to keep them, the way I plan on designing this base system means that each design is technically a completely different interior, between now and release could change a lot though.
Caesars Legion - CL bonuses are simple, the guards and troops from Area 51 will die for you if you ask them to, as in you will, in chapter 1, be able to hire up to 2-3 of them to guard you.
The Supermutants - I dont know why but supermutants are cool. Simple as that, only reason I want to use them for this is cos I think they look cool. To make it more general, this faction will also include ghouls, non feral of course. Their bonuses include being able to buy stealth boys, the base will be reconstructed as quick as BoS because of the obvious physical advantage of muties. As another bonus, I may be thinking of adding a DNA resequencer. This device will allow the player to rebuild their character, not only to ghoul or raider, or even just a new look but also any other races I add to the mod will be available on this machine (if I can get it to work that is).
Great Khans/Boomers/The Strip/etc - These factions and any I have missed wont be included. For the simple fact that I cant think of a reason to, if anyone likes any of these factions in particular and can give me ideas on the appearance of the base and bonuses then I will add them.
I will try and avoid any 'cheats' in the mod, like karma or easy items etc. but Im not promising anything and if you dont like being able to get things easy then dont use that part of the mod, simple.