I think there are several reasons for using traffic lights in reality that aren't currently represented in Simutrans.
1. Junctions with restricted visibility and/or tight corners (the latter requiring large vehicles to use both sides of the road when making turns). Also narrow roads, often on bridges or through tunnels.
2. Junctions where the flow of traffic is sufficiently heavy that if the junction were set up with minor side roads giving way to a major through road, then vehicles on the minor road wouldn't be able to pull out into the major road often enough (particularly if the 'minor' road is also quite busy). This could also be handled with four way stops, but these aren't generally used in the UK (although I have encountered a few examples used with traffic calming in 20mph zones).
3. Cyclist/pedestrian safety/convenience.
4. Junctions involving roads with multiple lanes. (Sometimes this is mitigated by the traffic flowing in bursts due to nearby traffic lights, rather than due to traffic lights at the junction itself).
1. Is not likely to be a feature in Simutrans.
2. Simutrans currently uses something resembling 4-way give-ways with good long-distance visibility, with no option of configuring major/minor roads as is normally used in reality. Actually, this sounds a bit like a mini-roundabout, except without the extra road width needed for a mini-roundabout. Maybe future changes could make the behaviour more realistic. The 'intersection_t' object Turfit has mentioned elsewhere could be used to implement this change. Another useful feature might be allowing vehicles to share a tile, and it might be sensible to account for this in designing an 'intersection_t' object.
3. Pedestrians/cyclists are not simulated to a sufficient extent for this to become relevant, and it would probably be too computationally expensive to do so.
4. This is a feature that has been requested before, and its implementation would probably also be based around the aforementioned 'intersection_t' object.
So in summary, I think the behaviour of traffic lights could be improved in the long term as part of replacing the existing code for intersections, and perhaps also vehicle movement in general. It would be interesting to hear what plans Turfit (and perhaps others) has considered for implementing these features.