If you could have allied yourself with Unatco/MJ12, it would have been cool to see all the MJ12 troops fighting by your side in later levels like Area 51.

Who would you have been fighting against? It has been a while since I've played all the way through DE, but if I remember correctly it is basically all JC doing the hard work and fighting. You become the ultimate badass and take on entire armies (sometimes through stealth) and if you weren't there the Illuminati would have been in real trouble I think.

So siding with MJ12 would have made the game end quickly because you just let them keep doing what they are doing basically. Now maybe siding with UNATCO you could have wanted to end the corruption/control of the organization by FEMA and MJ12 and made it a real humanitarian police force again. This could have then been interesting.

Yeah the game would have to of been redesigned pretty extensively after you arrive in Hong Kong for it to work. As it is siding with Majestic 12 would basically amount to not doing anything, just sitting back and sipping coffee.

True, but during the timeline of the first game, UNATCO was in MJ12's pocket. Remember the secret MJ12 lab inside UNATCO HQ?