Most of those can addressed by busses too actually.

Train has fewer stops meaning train reaches the destination faster

Bus Rapid Transit (BRT) or any bus line can have less stop for this reason. To expand on BRT routes, they can be dedicated lanes for busses, with right of way. They can be specific only for busses, and cars not allowed to use it ever or also mixed usage where certain rush hours are for bus use only but outside those hours can be used by other vehicles.

Train has ultimate right-of-way, and doesn't have to stop for pedestrians on the tracks, red lights, or other things

This can also be done with BRT routes.

trains in some cities, go under waterways meaning more direct routes than busses

BRT as well.

there's more space inside trains and usually more choice of seats. Standing is also an option which isn't allowed on most busses

Busses can absolutely support this. Paris has more open busses to allow more people standing or people with disabilities.

acceleration and deceleration are more predictable and comfortable

With dedicated BRT lanes, I believe that can also be done considering there's only bus stops that need to be slowed down on.

Nearly all metro light rail trains are powered by electricity, while many city busses remain diesel

I know technically electric busses are possible, but I'm not certain how feasible this is.

My understanding is that BRT routes are cheaper and faster to setup than trains, and can be upgraded to trains. I'm not saying BRT is better than light or heavy rail, but that should be a more common path for mass transit that is not utilized in the US.

Yeah. Busses join traffic. They reduce it, but traffic delays them

Having lived in several countries in Europe, in and around major cities, I have actually chosen the train over even the tube (aka subway) because it's significantly faster for longer distances (fewer stops, better acceleration) and in general more pleasant (a bit more space, actual open spaces outside the windows rather than just dark walls).

In my experience, trains, subway and buses have different optimal use cases: trains for longer distance (in a city context that's 20+ km) mass transportation of people to and from hub points in the city (they basically feed people to and from cities), the subway distributes people around the city center and buses are what feeds the trains and tube stations in the areas further away from the city center (were the subway coverage is far more spread out) and in cities without a subway they do the work of the subway (but they're less efficient than one).

Note that I'm not talking about the use case of trains to transporting people between different cities at long distances (50km+), but a different use case which is of trains for commuting which feed people from the suburbs and satellite cities to a main city and back.

Trams basically fit the same niche as the subway when there's no subway - they're much cheaper do deploy but can get stuck in traffic unless the tram lines are in physically segregated lanes from automobile traffic.

The way I've seen buses used in general is them set-up to going around to "every nook and crany" in residential areas plus with main tube/train stations as part of their route (often at the start and end of the bus line), so they have pretty windy routes and are a pretty slow way to do longer (5km+) distances since they're really there to feed people to and from the train and tube lines so are trying to cover as much of the residentia areas as possible hence travel back and forth in out of the way places and stop a lot.

Buses are also used in the city centers when there is good subway coverage but there they tend to just be secondary to the subway, generally just making up for gaps or other flaws in the subway network design (for example, parallel subway lines which only join far away so to do the trip with the subway you would have to go all the away around so the bus has a direct route) and as you get further out from the city center and the subway lines open up a spread out to cover those areas which end up too far from a subway station.

When the timetables of those things are properly synched it's really amazing: you can be living in a suburban area or smaller village outside the city proper, use a bus (or a bicycle, or walk) to get to the train station, catch a train to a main station in the city center and in there switch to the subway which takes you to a station near your destination were you just exit and then just walk to your final destination (with a proper subway service, in the central area of the city you seldom have to walk more than 500m to get anywhere from the nearest subway station) and you've spent maybe 30 - 45m to get from a house or appartment in the suburbs to an office in the center of a major city, zero chance of getting stuck in traffic, no worries about having to find a parking space, way less exposure to polution that if driving.

There could be dedicated separated bus lanes - I saw one in my world travels but never in USA. IMHO it is a better solution for short distance (i.e non-competing with plane) than inflexible heavy metro transit infra...