If you read through the City Based Demand thread, there are quite a few posts about connecting traffic (cargo and pax), how the calculations can be cut down. You can go back a few years...
SQL throught its magic can accomplish quite a lot, to identify the candidate flights for, say MPL-BOS. Let's say it comes up with 100 candidate flight combinations, ranks them and selects top 20 (or more or less depending how busy the route is).
Since route creation and destruction happens VERY infrequency, the above complex SQP does not have to happen every day, only say once per month.
Every day, the system would do its allocation among the 20 candidates, very similarly to what the system does today with direct flights. Additionally, the table of candidates would also keep how successful the candidate was in attracting passengers. Then at the end of the month, it would dump, say bottom 5, it would re-run the SQL and get new top 5 candidates to replace the 5 that were dropped.
So this way, the time consuming processing to identify the would be a background task run at low priority. There would be some increase in processing because the number of flights (direct and connecting) between say MPL and BOS would be higher. CBD may have a demand of 15 pax, and for such a low demand, probably no more than 5 candidate connecting flights would be needed.