I've been says for years they should replace it with a faction reputation/loyalty system tied to a Speech skill tree (Paragon options on the top branch, 'renegade' options on the bottom branch). What this would mean in the context of Andromeada's settlements, for example;
Reputation: Krogan 51%, Asari 29%, Geth 33%, Quarians 45%, Batarians -15%, Humanity 50%, Salarians 34%.
Skill Tree:
Charm-based Barter or Intimidation-based Barter (lvl. 4)
Charm Interrupts or Intimidation Interrupts (lvl. 5)
Intelligence-based persuasion or Charisma-based persuasion speech options (lvl. 6)
Intelligence or rather logic based characters will level up faster gaining a general (multiplier) boost to XP, have additional speech options with and gain reputation faster with Geth, Salarian and Quarian characters and characters from other races of a logical persuasion who respond favorably to quick-witted, well reasoned arguments and rational (logic orientated) charm interrupts.
Charisma-based characters gain a general boost to reputation amongst all other factions through charisma speech mutipliers and gain additional romance speech options. Charisma-orientated characters can opt for charm or intimidation interrupts which work well together with different factions - for example, when dealing with Krogan characters renegade interrupts and general assertions of dominance (e.g. headbutts) with charisma-based speech multipliers could be a great way of making new friends and increasing your reputation while logic-based characters will have a harder time winning over the hearts and minds of Krogan townsfolk.
Completing quests for Krogan characters and helping Krogan settlements increases your reputation and standing amongst Krogan and enables you to unlock bigger and better quests for better unlocks (unique gear, weapons, abilities and perks) which require higher prerequisite trust/reputation in order to pass speech checks. When your affinity reaches higher and higher levels you gain more speech options with characters of said faction, NPCs respond increasingly favorably and you gain more favorable prices at Krogan merchants and they start offering rarer stock.
Conversely completing quests for Turian characters/settlements arouses suspicion and affects your reputation with Krogan and vice-versa. Having low to negative reputation with a faction will result in increasingly hostile NPC reactions, higher prices and lower quality wares at merchants. At negative reputation factions will raise bounties on you and send mercenaries after you. Completing quests for Batarian characters for example while the most profitable will negatively affect affinity with all other factions because Batarian quests will generally involve raiding/pillaging/sabotaging the other settlements. Undertaking dangerous bounties for each these factions (off-world) can slowly help to rebuild your reputation for those in negative standing (i.e. community service).
Faction reputation also applies to romance and loyalty. For example high reputation amongst Asari would be pretty handy if you are trying to romance an Asari crewmember, etc, while having a high reputation with Krogan will inspire high loyalty from Krogan squadmembers on the battlefield which will unlock companion perks but attract disloyalty from Turian squadmembers and vice versa.
As you can probably tell this system would be much more nuanced and provide a ton of replay value and potential for role-playing. It would have more in-game consequence and would be a more accurate reflection of the personality, preferences and experiences of our characters.