The blue circle on the right side of the picture I posted on the first page is a horrible spot. The fog of war covers 1 more mountain tile south of the one you can see, 2 more jungle tiles south of the blue circle, one rice tile southeast of the blue circle, and the rest of the space that'd be in the cross is ocean (with no food tiles).
I chose #1 and #3 in what look to be poor places for different reasons. I hate settling on flood plains too, and I know there's not a lot of food there, but moving 1 tile NE doesn't help the food situation, and I'd exchange 2 grassland tiles for desert.
#3 is surrounded by jungle, and isn't fully utilizing the river. The jungle isn't an issue, with the great food resources and hills in my capital city I was able to build up only 10 or so turns later to be able to produce workers in 5 turns (on epic). So I beelined IW, cranked out 3 workers, and just chopped the jungle. So the health isn't an issue, and I use all the river tiles anyway between my 3 cities. So I lost a few turns of production and growth due to unhealthiness and producing probably 2 more workers than I normally would, but those 180 hammers and 10 or so food are trivial compared to the bonus of having what I think is 2 more tiles that would otherwise overlap.
I planned both #1 and #3 to simply produce commerce (my main city has loads of production and nearly enough food to support it (without having to link farms over). This does leave a dearth of overall production though, but there's a great spot off the map just left of #3 that has loads of food and hammers.
One thing I don't do well and probably should learn to do better is build a GP farm. I tend to turn potential GP farms into cottage empires instead.
But yeah, as Spearthrower mentioned, the AI builds towns far more tightly packed now. It really seems like BtS sort of gimped the AI's ability to pick good town spots. Another good example of this is to note where Barbarians place their towns - I'm consistently shocked by barbarian towns popping up in the dumbest places (not that they do much, but I remember being happy to see them plopping down in decent spots where they'd grow to size 2 quickly so I could just kill it and save a settler, now they're ALWAYS in spots where I raze them and end up placing a settler a tile or two over.