Need scoring solution

I was thinking that 4 boxcars would give you 1+2+3+4 points, but that would quickly spiral out of control, and only worsen the "10 and 0" problem. Perhaps the opposite, where the first boxcar is worth 4 points and the second 3, etc, but that would only mean short trains are relatively more profitable than larger train.

I think Corsaire's solution is very neat. It incentivises players to have approximately as many boxcars as other cars on each train, which would favour "6 and 4" over "10 and 0".

Here's a possibility:

-Mechanical defect cards: play on a train to cut a coupling when the train is x-cars long: this means that a player is immediately worried about having longer trains because he's more vulnerable to attack. Boxcars still allow you to score more points, sure, but they also add length to the train! I would have several different cards like brake or engine failure that force a player to discard cars from their train to keep train size in check, but if a player haggles with the other players to not get pounded on, maybe they can make a train that's a bit longer and score more points!
-Perhaps the coupling failure could lead to the train splitting into two trains that can be used later (an engine just has to go pick them up). Now, we have more smaller trains in play and penalties aren't all that bad: you just need another engine!
-ways to protect against certain mechanical defects could also come into play: have a brakeman, an engineer, and other cards that you can play onto a train to provide one-time protection. (Or permanent protection to that one train with the engine on it. An engineer could protect against engine failure which forces you to leave a lot behind, but maybe they can't fix a coupling failure, so the new train that falls off of it is now unprotected from the engine threat, etc.)
-OOOH! What if the trains that separate off can be stolen if you have the right kind of engine to go pick them up? Or just any old engine, for that matter? That sounds even more fun and nasty!

I think you're onto something here...

I ditto the comment about creating an incentive to cash in early. Make it riskier to have longer trains.

Here's another thought: Make the limit not be a solid number, like 6 box cars per train, but rather be a ratio, like up to 2 box cars per 1 non-box car.