You are forgetting an important factor - some terrains and improvements get additional bonuses from rivers. Overall, a city by a river is already a much better deal.
I disagree. While river tiles are definitely better one doesn't have to place a city near a river to gain the bonuses exept to build the aforementioned levee. I'll try to explain again. First the city near a river (or any source of fresh water) receives only a little bonus of 2

while fresh water in real life is crucial for a city to grow considerably. Second the city on a river doesn't receive any trade bonuses while I'm pretty sure in real life the riverside city would be much more favourable than the one at some distance.
There are however some problems as noted by cfeyyaz: AI does not prefer to build cities near rivers or oceans but it tries to cover more resources and what about fresh water sources that can't be shown due to the map scale. I don't know if it's possible to solve the first problem but I don't see how the second one is since fresh water shortage in the game doesn't deny the city growth: there are plenty of other health bonuses.
And some additional issues in 3.25 I'd like to discuss.
1) Why is it
so frequent even possible when my spies are caught on CIV A territory when they are moving through CIV A to mess up with CIV B?
2) Is there a way to know which building is created by a ministry so I don't waste my sabotage building mission? (espoinage)
3) Holy places (the ones that receive

for cities) are so very powerful. A little nerf plz?
4) Supercarrier promotion is not available to carriers.
5) How do bombers earn experience? Why not like artillery when bombing health points?
6) Why is it possible to upgrade 20

infantry to 24

semi-modern infantry when 28

mechanized infantry is available but it's not possible to upgrade 24

semi-modern infantry to 28

modern infantry when 32

IFV is available.
7) Is this model (shock troops) correct? Magazine all right? What gun is this?
8) What is the purpose of gunboat ships? Can't imagine how I'd use them.
9) AI leaves a lot of cool units in the rear. For example, it would protect all cities (even the ones that are far away from the front) with 3 riflemen when fighting the main battle with outdated fusiliers. Can't it calculate that's not necessary?
10) AI civs have low income in the trade table. When I try to sell another civ the resource I can see that they would pay me more if they had more income.
So I thought that maybe it's a good idea to limit fund allocation to research/culture/espionage with civics like it was done in civ2-civ3.
11) Another idea to counter the everlasting expansion. A chain of very expensive buildings (or projects so they can't be hurried) that become available with techs and after completion give the city tile

or

. So instead of building expensive military or inefficient research/wealth/culture there is an option to improve the existing tiles rather than to conquer more tiles.