I've been Humankind nonstop since it first launched, but only recently have I tried to play it on a higher difficulty. I can deal with the expensiveness of raising and spending influence and whatnot, but when it comes to dm independent people, I have absolutely no defense whatsoever as they easily kill my units and then destroy my settlements with little to no opposition.

I've had numerous games where even with a larger force, I've suffered consistent defeats from the like of chariots and swordsman while I'm still trying to create my own. By the time I have the both the tech she the resources to create the necessary armies, I've lost more then half of my territories before I even reach the classical age with as many 10 to 16 enemy units from the independent tribes all breathing down my neck and it's only the first 67 turns off the game. 

It also doesn't help that I'm playing on Metropolis difficulty which is challenging enough. If it just that my playstyle is wrong, because it's send like no platter what I do, even I don't directly engage them, their units automatically antagonize mine and force to into a corner for the sole purpose of killing them and depriving me of a sizable defensive line. It's incredibly soul draining just trying to sustain my territories for the 120 turns (yes I had 3 independent territories harass me for 120 turns each) it takes for the factions to die out.

I love playing this game, but for me it seems almost impossible to play any difficulty higher than town which really sucks.

Can someone help me?

You must be unlucky to get so many aggressive IP. The early chariots sure can be deadly if you don't have spearmen. The peaceful ones will totally ignore you. Try seeing IP as opportunities. You can get free cities by either capturing them (if newly founded city still has 0 pop it's free picking) or assimilating them. If you have to fight them, it doesn't matter how many in total are running around, their armies hvae only 2 units till much later and they are late to get reinforcements. Just have some nonscout armies and counter units if possible. They are a good source of points for militarist stars. Besides having military you can protect attached territories by connecting administrative centers to main city with districts, then those administrative centers will be inside the walls and they can't ransack.

I managed to convert 1 city in playthrough. But there were times where I was still a neolithic tribe and my lands were being pillaged by chariots or my units getting shanked by warriors as scouts. 

I tend to leave the IP alone as much as possible, but as soon as I do, I get accosted by mercs or units that deliberately follow my retreating units, herding then into kill zones to then slaughter them 

On lower difficulties the IP tame, but on Metropolis and higher, Im losing 8 units every other turn because they're harassing me knowing full well I is almost impossible to build as many units to counter them.

It's also worse when researching tech on the Metropolis difficulty because a unit costs nearly 10k to buy (because EVERYTHING is expensive) and my population is too low to spare additional forces. 

At first it was mind boggling, more it's like I'm expecting to be dunked on by the minor AI while trying to compete with the major AI. 

I honestly wish there was a toggle feature to control IP spawning and aggression, because this is ridiculous.

Independents during Neolithic era? That doesn't make any sense, I have played for hundreds of hours on Humankind difficulty and never ever seen that. Only mammoths and bears..