I like your idea, this is a good suggestion.
Independents pop are too strong in the early game and become insignificant in the latter part of the game.

3. Make independent people UNIQUE. I would suggest each independent people provide Unique bonus to the player (or all player, if the affinity is still capped by 100) that has the highest affinity to them (like civ6 city state system), the unique bonus should be strong enough to make you keep the independent people alive rather than destroy it for good. And the player with the highest affinity can choose not assimilate the independent people and enjoy that bonus.

One thing many have said that they miss from endless legend was the unique units. I think that one simple way to improve independent people is to provide their city with two things:

1. Make their administrative center/main plaza be able to have unique district built in that city. This reflects their culture merging into your own.
2. Give them the ability to produce a unique unit that you can buy as mercenary.

I would add that this can give a really huge impact to the choice between half cost for mercenaries and half cost for assimilation, or better yet can serve as a follow up to that choice the same way we have for government.

I also would like to see more independent formation and relationships. For example, we can see the inclusion of world congress system, like in CIV 5.

That being said, I kind of would really like to see many of the current independents become full fledge civs, such as the:

• Mochicas, with their brick temples
• Scots
• Inca Quechua (this is a pet peeve, calling the Quechua the Incas is like calling the Americans the Presidents or the Egyptians the Pharaohs)
• Kingdom of Kongo
• Tamil, a thalassocratic empire.

I agree with chariots things. You advance to ancient era have only scouts didn't even research the calendar and independents are chasing your scouts around on chariots while the wheel won't be invented by anyone for the next 1000 years or so. If you beat the chariots why don't you salvage the wheel technology from them?

Second it, if you play on large or huge map then independent spawn like 3-4 cities around you while you barely have enough influence to promote 2nd outpost to city. Why bother? Just stalk the independents and when their outpost is promoted to city, nab it since it's unguarded and even 1 scout can net you a free city. The camp is/can be promoted to city like in 2 turns, you see empty territory move your scout to another and the next turn there is a city in there? Like what?

Third, as it was mentioned, there is no merit in leaving independents be. EIther you assimilate them or the AI does. There is no such thing as leaving independents to spawn units for you for you to hire them if your money is good and industry suck or you don't want to use your pops to make units. I liked that in ES2 once a player hit max reputation with minor faction there was no stealing, you had to go to war with them if you wanted to assimialte them and have their bonuses. It could be changed the if you want to assimilate them they would have to be in your sphere of influence or share religion with you.

ATM i would like to have option to disable them completely since many times they are simply ruining my game experience since there is like no merit in stockpiling influence to promote outpost to city since you can get easy cities by nabbing independent camps.