pretty sure the area around malshej ghat is one of those bio-diversity hotspots, which essentially means a strict no-go area as environmental clearance+protests from environmentalist and environment conscious people will delay everything.

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If distance saving is great (about 40%),then taking elevated route over the bio diversity spots may be studied and adopted if feasible.

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would be difficult. Western Ghats are horrible places to construct railway lines, which is why KR will go down in IR's history as its greatest engineering feat.
elevated route would be exorbitant, and besides moving heavy equipment in place and creating embankments while constructing will negate the whole purpose.
The length of the line proposed is a bummer though, should have been less; it seems a wasteful expenditure just to appease people staying in the region rather than well though out investment.

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I guess Nashik-Pune line will only be beneficial to the people of enroute towns and villages. Nashik is in north direction from Pune and it is not a junction. Moreover, trains coming to Pune from North India mainly use Vadodara-Kalyan route or Bhusaval-Manmad-Daund route.

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Pune-NK-MMR opens up shorter route from Pune to Central/Northern/Eastern India

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