Lack of a 'transfer' function between registrars. At the present time it seems like you have to 'delete' the domain, wait an unknown time for it to clear out the database, risk someone else grabbing it, and register a 'new' domain at full fee. And if the new registrar is just as screwed up, doing the whole thing again. Lack of deposit accounts and invoices. Credit cards are ok for individuals and small companies, but anyone planning to handle more than a few domains it becomes a pain.
Web interfaces suck.
E-mail templates and responses are easier to archive, automate, and generally integrate into our existing processes. Web interfaces generally require hiring a body to type duplicate data into yet another system. Failure to understand the standard rule of new competitors entering a market. Personally I expect most middle to large ISPs to eventually become registrars themselves. So they're waiting for the test phase to finish, before taking the plunge themselves.