Short version:
The running cost are realistic, but the map size isn’t.
In reality trains beat trams / trucks on long distance, not 2-5km. Nobody would be stupid enough to use a high-speed train like ICE or TGV for a line from cologne north to cologne south or London North to South station.
Another point is that passenger choose between car, walk and train ONLY by speed. I think there should be some “money” factor.

What do i suggest:

• bigger maps 😀
• change balance (running cost) of trams and trains.
• change acceleration and top speeds (to be more playable, less realistic)
• add an “travel cost” factor to path finding – making long-distance car travel less attractive.

Long version:
Trains were only useful in 1850 for distances over 5km with no stops. The averange distance in my living area is about 5km for interurban train (rapid city transit), 10-15km for city-to-city connection and 50-70 for high-speed trains.
An Example: The city I live in has a area of 16x16km, with about 4-5 train stations none of them connected by inter-city lines. Historically they (taa-daa!) were connected by trams. Today these got replaced by buses or faster trams.

Some simple math – assuming a line with 9min (for the train) end-to-end travel time including stops:
Cost for a small train (6 cars passenger) at 1850:  201k + 6*25k = 476k
Running cost: 120k + 6*16k = 226k / year –
Capacity: 72
Estimated frequency: 18min (which means average wait time is 9min(!) )
travel time for passenger: 9min + 9min = 18min (time to walk to station not included)
Infrastructure cost: 350-550k, running cost are also more expensive than tram…

Equal amount of trams for 72 passenger = 14 trams (70 pass)
Buying cost for 14: 700k
Running cost for 14 Trams: 70k
Estimated frequency: 18min (end-to-end) / 14 * 2 = 154 sec (which means average wait time is 75sec )
travel time for passenger: 18min + 1min = 19min (picked up at his door step)
Infrastructure cost: 70k almost no infrastructure costs.

What does this mean? Trams are better:

• scalable (buy as much as you need, 1 by 1)
• less infrastructure needed
• almost no maintenance costs
• 1/4 running cost

On top, I tried connecting 2 trainstations in 2 neighbouring citys by train and by tram, and the people preferred to go by tram… >:O

1. Having more running cost on trams makes huge loss for some In-city branch lines.

2. Trains are much faster than trams from 1930s, and not affected by private car traffic

Faster means more opportunity to earn income and grow cities, essential to build big cities.

(you can still use trams for not-so-big adjacent cities, but that’s realistic so no problem. separate cities are much better with faster trains)

3. Tram/Bus stops have very limited capacity while train stations have enough capacity to serve one line, especially big one.

4. Trams are often ‘stuck’ with road traffic AND public transportation itself, making it annoying especially on large maps where busy checking other lines and building more lines.

5. Trams are even not enough capacity for in-city lines on big cities (over 1500 pops) around year 1950, They even have less than 20s frequency and not enough.

I think loading/unloading time needs to be fixed (faster for more cars or doors attached on that train) because that makes trains much better while not nerfing trams so that could run branch in-city lines without huge losses

Trains don’t cost as much to run in a year as they do to buy a new train. That’s ludicrous.

• high capacity goods lines (e.g. wood to saw mill, oil to refinery)
• inter city connections, after 1906 with 100km/h trains (1 -2 Cities distance, like (Cities A-B-C-D) A->D, A->C)

Strange thing I noticed: There are small passenger railcars in game, they would make much sens to replace the high-duty trams, but there are no small stations available to fit them. Building a 160m platform for 15-30m railcar is just uhhm, stupid.

1. Having more running cost on trams makes huge loss for some In-city branch lines.
nope. In total the tram has 1/4 of the running costs of a similar train. – Even with a 12-car train the running cost is 1.33 for each passenger seat, an equal amount of trams has 0.97 per passenger. (And this do not include the running costs for the stations! Neither you can fill this huge train as easy as the trams.)

2. Trains are much faster than trams from 1930s, and not affected by private car traffic
They are. By people choosing car, not train. The really funny thing I experienced is people do not use private cars, if there are intercity-trams. Opposite is true for trains. (BTW: another big issue: The assumes from 1930 that every citizen has a private car…. Its like “ohhh. It is 1930, let us all buy a car! I take 8 for my family, so everybody has its own!”

Faster means more opportunity to earn income and grow cities, essential to build big cities.
Try trams. You will see the cities grow even better for some reason. I had cities grown to pop. 1000+ in 1866 only with passenger trams on hard focusing on one city, something I never managed with trains.

(you can still use trams for not-so-big adjacent cities, but that’s realistic so no problem. separate cities are much better with faster trains)
I say this is just wrong. Give trams a try and you will see. Later 60km/h trams are capable of connecting 4 near cities or 2-3 “far” cities…

3. Tram/Bus stops have very limited capacity while train stations have enough capacity to serve one line, especially big one.
Right, but 1 train = 14 trams, still much cheaper. Please have a look at the numbers I gave above.

4. Trams are often ‘stuck’ with road traffic AND public transportation itself, making it annoying especially on large maps where busy checking other lines and building more lines.
My experience from my tram fever games is: there is much less to no private traffic, when using enough buses and trams. – With trams only you can reach up to 98% coverage…

5. Trams are even not enough capacity for in-city lines on big cities (over 1500 pops) around year 1950, They even have less than 20s frequency and not enough.
Right. There is a point (around 1880-1890 in my games) where a single tram line is maxed out by cities with 1200+ pop. But try 2-5 separate line connecting cities each on its own road each. Works perfectly fine up to 3000+.

And private car should not be problem when you use train extensively for inter-city transportation. You even could destroy country roads to prevent private cars, but good ‘train’ lines even make only few private cars on the streets

Also note that you can achieve over 95% usage with trains (no inter-city trams) too. by choosing right vehicle. commuter EMUs(or DMUs) are best for adjacent cities. Ae 4/7 and Re 4/4 are also good before commuter trains are coming out. faster, heavier trains are better for longer lines (A from C or D or E in A – B – C – D – E Scheme)

Maybe I misunderstood you, but currently it is exactly the opposite as you say. Trams have in all areas lower running cost than trains. My Point is that the distance between cities is to small. On most maps the distance between cities is as width as 1 city. – For example the distance from west border of city A to East of city B is as long as city A east to city A west. – Thats what doe not make sense in my opinion and make trams so over powered.
Tram = low investment (can stop on the road, does not need it own tracks etc), high acceleration, agile in cities, but capped at 60-80km/h (which is realistic, trams here in Germany are capped at max. 80km/h, usually 70km/h. only some Rapid transit lines have 120km/h with small modified vehicle)
in-game advantage: higher frequency: more passengers.
Train: lower running cost, lower acceleration, needs straight tracks (which makes using inside cities impossible), but a higher investment.

And private car should not be problem when you use train extensively for inter-city transportation. You even could destroy country roads to prevent private cars, but good ‘train’ lines even make only few private cars on the streets

I know. But I bet you can get even better results with trams, using trains only from 1950+.

Buses / Trams in my game are exclusively for inner city travel and trucks for the closer city to the industry.
Everywhere else is trains.

I have also never (well maybe once to test) created a city to city tram or bus line, just because I don’t want to play truck fever 🙂

I’m not chasing the billions, so long as its in the green (even barely) I am happy.