Mangalore will not get the intrastate connectivity it needs until both Shiradi and Braganza are optimized which is in the hands of SWR.
Both SR and SWR have really not touched the tier-II cities in last 10 years in terms of serious infra developments(Only UBL and ERM are getting just one new pit line each).
Mangalore could be resolved on the lines of Goa and Varanasi, wherein SWR can takeover MAQ through Padil while SR/KR controls the ULL-MAJN-JOKT-NMPT section thereby retaining the KR/SR contiguity. SWR in the meantime gets one more CDO...
more... and can use the pit lines for its own trains instead.
Should SR retain MAJN, they can develop additional pit lines to cater to future trains while maintenance of present trains can be shifted to Chennai/Trivandrum.