Regarding your comparison to real life, the thing is most of what you miss don't necessarily work with the game scale and mechanics, which make balancing a bit tricky, especially if you want material that respect their real life specifications.
For example on passengers trains, the best ones would almost always be trains that are fast to accelerate, have a decent max speed and good capacity/loading speed, because of the relatively low distances between stations. Add to that the fact that the game make no differences between standing or seating passengers and the best solution for your lines will basically be a real life commuter or some regional express trains, even if you consider your line to be a long distance one. With the very basic economy of the game, and from a profit perspective, you will have a single best train for the majority of your passengers lines, which may not even be the one with the greatest speed or capacity, but the one capable of transporting the biggest amount of people every month.
For the same reasons, some trains will never be the best at anything in TpF, like for example some high speed train with slow acceleration and slow loading speed, because the maps are usually not big enough for the difference in speed to make up for the time lost during the loading at the station and the slow acceleration to max speed.
Of course it's a bit of a generalization, and it depends on your map size and settings, but given the economic system of Transport Fever, sometimes you have to forgot about the "best" for the sake of variety.