In comparing both of your saves, keep in mind a large chunk of the advantage from S1 comes from Oracle -> Civil Service. Not only is it an instant +1000 beakers but the Bureau bonus also carries hard.
Your land seems overall much better developped in S2. However, 4 important city spots remain to be filled in the East. Most of the island, if not all, should be settled at this point.
If I'm seeing right, Nagara is not working its Fish and Harihara is not working its rice in S2. Meanwhile, both cities are slow building Courthouses and working a couple of mines. This is probably wrong in a few ways.
- First, you should take a look at your cities maintenance. I doubt the courthouses are an important item at this point. Simply because you have access to courthouses doesn't mean you need them. It was a different thing in the last game when you had 19 cities.
- I understand you're working mines over food tiles to avoid growing into unhappiness and work as many cottages as possible. Remember you are running Representation. If you want to maximize your science, then growing to happy cap is a good idea but the final 2 pop points should be used by running scientists (and then your food is useful).
- However, the island is not settled in its entirety. It is not the time, yet, to go full science mode. It's possible you should still be working on multiple Great Scientists (looking at you, Nagara) but there is no reason to avoid growing into unhappies. Your cities can still function at happy cap -1 and do whip cycles every 10 turns or so to help with the expansion. Especially so since there is at least 1 unclaimed happy resource in the East.
- The point when you should go full science is when you are done building settlers (be it because the island is settled, or the locations that are left are not worth the maintenance and the tech delay)
People have very different ideas on how to approach this map and what settling pattern to use, so take my opinion with a grain of salt.
I think it's important to recognize early that your capital's production towards settlers is low. Yes, you claimed a plains hill but your best available tile is 4 yield only. As far as production goes, this is very subpar.
A direct consequence of this is that the main job of City 2 should be to have High Production towards Settlers. This means forests and high yield tiles, like the BFC pigs that you abandonned.
So, in S1 you went for a marble grab and in S2 for a cottage centre with City 2. I do firmly believe that Angkor Thom in S2 (so your 3rd in that save) is the best location to fulfill the purpose that should be assigned to City 2 : building settlers.
Quite importantly, that spot also serves as a spearhead towards in the East. If you building workers/settlers in this centralized position, they will be quickly in position. It also allows to expand your road network only 2 or 3 tiles at a time, so your workers can be more impactful.
Marble : Props for roading in advance but I can see you want to settle the same spot in S2 as you did in S1.
I think this is a situation where you should take a moment and use the ALT+X function to dotmap properly (CTRL+X to show/hide).
It would seem to me that the rabbits belong in crabs/horses/oasis city and marble/sheep should be riverside.
Remember, you're building Courthouses in the north for fear of maintenance. While I believe they are premature, Isolation is a scenario where you want to claim as much land as possible, using a few cities as possible. Maintenance and the cost of settlers is certainly to be taken seriously.
Stone : You went for it with City 3 in S1 and City 4 in S2. Both times in the same spot.
I kinda hate it. I also hate settling on the stone to save on worker turns, by the way. Settling a no-food city has a huge cost, especially in isolation (see above). It is also a relatively early city (even as 4th) that will not contribute to the Empire as much as other spots.
First and foremost : accessing the stone is only relevant if you have a city ready to start on the Pyramids. At this point, that city is not contributing settlers/workers anymore. The earlier this happens, the more proportion of your global production effectively disappears. I would consider sheep/marble and the 2nd pigs as must claims and be very hesistant to settle for the stone before those. So, I would only consider the stone for city 4 or 5, here.
I would also always claim the stone from the 2nd ring, so as to have food in my city. I chose to backfill and settle on the ivory (+ 2nd ring fish). Sylvallewelyn went for it with his 2nd city in a spearhead position with lots of 2nd ring grabs (+horses + rice), which I find quite smart.
Both of those locations are incompatible with some of the city sites you've used, and this is natural. They're also explained by different capital locations that come with different needs, problems and solutions.
I cannot vouch for the best settling pattern on this map (no 2 players did the same in order and locations) but it is a very fine example of
Why Dotmap Matters. Especially in isolation where you are not competing for space with AIs.
I won't touch the specifics of the tech path in Isolation but I suppose some things could be said. I'm also unsure how Monarch should affect it (Oracle -> CS and all).
My main point is that only a limited number of techs are truly needed to sustain the colonization. Once they are acquired, it is acceptable to take all the maintenance hits at once. Research can literally be stopped until all the cities that Player is willing to settle have been planted. At that point, the island is ready to be developped
en masse and gear towards Astronomy
.
Hope that helps, cheers
up with 
and the cities grew
