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No one cares what you bother about or don't. There's a policy and it's being followed plain and simple.
No train going towards Kota from Mumbai side can ever skip Vadodara. But it is skipped by trains going to Ahmedabad (notably 2 Duronto Trains: Ahmedabad Pune Duronto and Hapa Mumbai Duronto)
No train ever skips Kanpur but Prayagraj New Delhi Humsafar bypasses Kanpur....
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No train coming from Jabalpur side ever skips Itarsi, but trains coming from Bhopal do.
Balharshah and Deen Dayal Upadhyay are unskippable anyhow. Because they are Zonal Exchange points too, Jhansi has also been considered under same category.
Bhubaneswar is unskippable for all trains except Puri Trains because the source is nearby and you won't need crew change immediately. Neither is it a Zonal Exchange point.
Exceptions are there when source is nearby Technical Halt. Which is not the case here with Vikramshila Express