When there is ad valorem pricing, large transactions get charged more. So it's essentially a cross-subsidy program where large transactions subsidise small transactions. It is not clear why such a subsidy is worth implementing.
The pioneer in switching to a flat tariff was NSDL. Most of Indian finance does not, at present, use a per-transaction price. An interesting recent development is an announcement at Kotak Securities, that they will offer a flat price of Rs.20 per trade or Rs.9 per trade (with many caveats). Also see the Business Standard story on this. As with the NSDL tariff structure, by the time India gets going on doing things right, the prices that are seen are really low by world standards.
The securities transaction tax is, of course, ad valorem, and Kotak Securities has to add this into your contract note even after they have shifted to flat pricing. Update: Rachna Monga has done a story in Business World on this (unfortunately, is not a permalink, and requires a registration).