For example:
1) Save Cass - Enable you finish Birds of a Feather without sacrifice Cass.

2)Brotherhood House Alliance - Enable you finish The House Always Wins without eliminate BoS.

3) FoA NCR Alliance - Enable you to persuade FoA to help NCR during final battle, alter the ending of FoA.

For me it is great because I can proceed the quest without hesitation, but then it defeat the purpose of "current" design. I heard some of them such as the BoS House Alliance and FoA NCR Alliance, the speech challenge option was original design which cut from the game.

As far as i know the FotA alliance wasn't cut, it's just buggy. Oh well, at least that gives you a teeny-tiny reason to side with the legion.

Within reason, I don't think there's anything wrong with any MOD, no one has to download them and if they do and don't like them, they can just disable them.