Fees
Is your direct debit provider going to charge you a fixed or percentage based transaction fee?  Generally, direct debit providers charge a fixed fee for bank accounts and a fixed and percentage fee (to cover their merchant costs) for credit cards.  Generally all fees can be passed directly onto your customer, but talk to your direct debit provider.

Fixed and Variable debit
It is essential your business has the flexibility to debit your clients either on a fixed schedule or variable amounts as required.  Don't limit yourself or your business!  Also make sure you can collect fund "on demand" - being able to only collect funds on a certain day not only limits you but may also be inconvenient to your customer. 

Support
A good direct debit system should be available outside of the standard work day.  Make sure your direct debit company is available when you need them and just during typical "office hours".

Value add
The majority of direct debit providers provide a similar product and they are all very good.  But what are the little extras they offer to make them stand out.  Do they have strategies in place to reduce the number of failed payments due to insufficient funds? Or can they implement a system that is a variation of the typical direct debit?  Is there any customizability?