I don't think fixing the performance costs is possible.
If we keep the concept always best TRs possible.
But if we change the concept maybe it can significantly enhance the performance, don't you think?
This is why my first idea was to check a random approach to see the performance gain. AND with max 16 routes probably dragged the performance to a worst stage, but in LoR (with 8 max TRs) performance was only significantly affected in Huge Modern Era (at least on my 64-bit OS, 2.4 GHz, 6 GB RAM pc under minimum graphics, a mediocre processing power by my guess, I don't know much on this subject too). Passing of turns that took like half a minute. Size in total cities: something around 300, and average 5 routes/city.
Reducing the total number of TRs and/or trying a beter approach at calculating the TRs may do a substantial gain on performance, at the cost of not having the best results (which is what makes it ubearable to performance now), and keeping most of the other game features intact.