Giving allegiance systems a good reputation

They say that reputation is everything in life and the same can be said with games. Nothing makes you decisions more meaning full than long term influence with characters. Whether it be simple relationship goals like in Stardew Valley or XCOM 2's resistance dedication. There are several things that make allegiances feel real.

1. Reprocusions

Fewer things scream realism like long term repercussions for your actions. Did you skip out on a date with your virtual partner, she may no longer trust you. Did you abandon the mission supplies that some refugees needed? They may throw you under the bus in the near future. Create systems with conflict of interests and clashing goals which result in new enemies. use this to set up dilemmas especially if there are multiple parties to which you can push your allegiances. additionally reputation is a factor of work done/time. if you spend to much time doing nothing, the person or persons wont like that and you will lose reputation and perks.

2. Benefits

Encourage your players to help these groups by putting substantial benefits at irregular intervals. you can do this by (along side regular rewards like gold, love or items) give them points on a "reputation" track to help to visualize their standing with an organization and what grade of gifts they should be receiving. Have these benefits point towards a end of game event and have them help you when that time comes

3. Story

Furthering a line of quests with a particular organization such as one of the guilds in Skyrim usually furthers the story. But often the story influence is limited to just one line and dosen't influence anything else. have it influence the main arch or your conversations with other groups. Additionally you can have it change your character. operating with the Thieves guild could have your characters dialogue change to incorporate more sinister overtones or working with the Church might make you more likely to add religious text to your conversations

Problems with these ideas. These ideas present massive changes to a world. Like character, story, and influencing features. That's why its so difficult to properly implement unless your entire game is based around them. Role playing games like Warhammer 40k and Pathfinder are great at this however as the DM (dungeon master) can change peoples reactions on the fly. Just remember to give your factions a little long term weight no matter the circumstance or else people will feel that they are useless.