The issues you are talking about is much greater than just land raiser, collective minds and negative influence. 44 cities is a product of how settlers work and would not be possible if settlers was removed as I doubt anyone can conquer 44 cities in that timeframe, except with maybe heavy independent people exploiting.

Negative influence have quite big stability impact as it is turn^2, that mean in 10 turns you should have a -100 penalty and in 20 turns you should have -400 penalty which seems quite resonable, but given how quickly you win that penalty is too slow, but that is not the penalty fault but just how quickly it is possible to end the game.

The tech tree itself may have a look at, here is the shortest tech path to tend the game right now from my knowledge:

As can be seen only 15 out of 30 contemporary techs is needed and only 29 out of 92 techs are needed in total to end the game. 3 end game techs are linked directly to rocket science and the exosuit is on the same tech path as the one towards rocket science and the fusion power line don't have any pre request except being in contemporary. The tech cost of an end game tech is only somewhat more than other contemporary techs instead of being several times more as in Endless Legends. Since tech cost increase with number of techs (1% per tech), by researching less tech you pay less for each tech compared to a more "ordinary" tech path in which you get majority of the tech before you end the game.

The game make it easy to spam cities and those cities benefit from huge 5% per resource manufactories which lead to a huge economy and quick era stars. Land raiser build the economy and buiders due to getting 10 stability per district can keep building makers quarters nonstop, collective mind then turn that industry into science, both using the industrial multipliers and then the research multipliers on top, leading to enormous science and combined with the overall low research cost and few needed technologies lead to very fast wins.

So I see many things that may need a look at:

• Settlers which make city spamming possible.
• Manufactories which give massive multipliers and huge stability boost.
• The tech tree, cost and requirement of the end game techs may both need to be increased by a lot.
• Builder and scientist affinites.
• Maybe also era stars in general, maybe too easy to advance quickly through era even if that is mostly caused by above.
• Obviously stuff like cultures, Egyptians especially seems too good.

Settlers are so problematic and lead to weird game-y scenarios, even in less exploitative cases than this one. I understand the motivation for them (not wanting to create mid/late game cities in an infrastructure hole) but the current Settler unit opens up way more problems than it solves. There needs to be a fundamentally different solution here and I think there are a variety of approaches. The simplest one from a coding angle might be to change how industry/buyout costs work for infrastructures specifically. A granary or irrigation system or barracks should be a simple project in later eras. If the cost formulas were changed so that, say, building a granary in Early Modern were a cheap buyout then you could eliminate Settlers entirely. Build/capture a mid/late-game city, drop a thousand or so gold into it to purchase basic (early era) infrastructure and you're good to go. The scaling would have to be tested out, of course... an infrastructure shouldn't be *too* much cheaper a single era later or else that promotes its own game-y behavior. But I think the basic idea is workable.

And the other stuff too. Settlers are just one part of it.