Exactly, puzzle pieces can't perform traffic-type conversions; I had tested this long ago, considering making RTMT puzzle pieces; this solved two major problems, the no-access zots and the textures that can't be wealth-dependent for lots (as lots have their own wealth level), but was basically unusable as conversions couldn't be performed.

And yes, subways shouldn't intersect in crossings, one should go under the other. I don't know if it's possible for the game to ask whether to make an intersection (like for highways), but it could still be enough if it could be left to the player making the connections, if needed. And I don't think rail is a good example, the intersection looks just stupid, with that circular track around it (sometimes trains even run around the intersection, when they could just run straight), that for the subways could be much simpler, just two non-intersecting tunnels (connections between tunnels would be independent of the intersection, just short diagonal tunnels - or instead straight in the case of a diagonal intersection). Basically there are four types of subway intersections that need to be changed, straight, diagonal and the two straight-diagonal combinations). Another needed thing is BATs for the non-intersecting tunnels. I think this is quite easy (they need not show subway automata running through).

EDIT: Existing cities may not be affected, if this could be a new type of intersections, while the "old" ones can be still functional (though not possible to be constructed anymore).

And yes, subways shouldn't intersect in crossings, one should go under the other. I don't know if it's possible for the game to ask whether to make an intersection (like for highways), but it could still be enough if it could be left to the player making the connections, if needed. And I don't think rail is a good example, the intersection looks just stupid, with that circular track around it (sometimes trains even run around the intersection, when they could just run straight), that for the subways could be much simpler, just two non-intersecting tunnels (connections between tunnels would be independent of the intersection, just short diagonal tunnels - or instead straight in the case of a diagonal intersection). Basically there are four types of subway intersections that need to be changed, straight, diagonal and the two straight-diagonal combinations). Another needed thing is BATs for the non-intersecting tunnels. I think this is quite easy (they need not show subway automata running through).

EDIT: Existing cities may not be affected, if this could be a new type of intersections, while the "old" ones can be still functional (though not possible to be constructed anymore).