The success of any ecommerce or subscription based website depends on the efficiency and reliability of the credit card gateway provider with which you have linked your site.

Of all the factors Price/Cost is the most important to consider.

Higher Upfront fees and lower per transaction percentage or vice versa?

 Most providers have an upfront component on signup which might include a deposit amount (like ICICI bank) and a percentage per each transaction cost. Eg. Rs.25,000/- Upfront cost and 5% of each transaction. 
Some gateways like Paypal don’t charge any upfront cost and their percentage is also low but they do charge an amount for withdrawal of money.

Should you go for a higher upfront payment and lower percentage or a lower upfront payment and higher percentage?
If your transaction volume is going to be very high then a lower percentage might save you a lot of money in the long term although upfront payment would be higher.

The following table gives you an idea of the various payment structures of various gateways Indian and Overseas.

Of course there are other gateways  but the above are the ones which we have had experience with.