civ2 made a step in the right direction, limit rails to production increase only, and only 50% so that squares with only 1 prod doesnt benefit. No trade bonus! and put in a maximum capacity. The movement thing, just make it like the old airlifts of civ2 (never used airlifts in Civ3 due to rails
) you can move a certain number of units by hitting T (for train
) and choochoo them to a city that is linked by rail, this ends the units turn (load on and off) voila!
it needs perfectioning, but its IMO the best idea I've seen here so far