Issues I can think of offhand:

• Lack of redundancy. With two redundant routers you can't trivially share the same DHCP range across both without problems. ISC dhcpd has a failover protocol where two redundant servers communicate with each other when they assign a lease.
• Too simplistic. You don't get as much control over the options and setting you can assign via DHCP with the Cisco router dhcp implementation. For example I don't know of a way to do vendor space DHCP options. If you're dealing with a trivial config thats no big deal.
• Logging, control, state. You can't get much information out of the router easily in terms of what requests its seeing and responding too. And to make things worse all the DHCP client state is stored entirely in memory, if the router reboots it will forget all the leases it already assigned, and may try to re-assign those same addresses to new clients.

There are more, depending on the exact setup you're deploying and the level of complexity. (DHCP Option 82 for example)

Carnegie Mellon's NetReg is an open source system that provides a pretty complete IP Address Management toolset, including management of DNS & DHCP configurations for ISC bind/dhcpd. It can manage ISC dhcpd's failover configuration, and multiple server groups, etc.

Rather then just repeating what I've said before when the subject of IP Address Management came up on slashdot, I'll just link to it.

Note: While the project has been pretty quiet for quite some time now, thats mostly because its the system is very stable and there hasn't been a lot of major new development in the last couple of years. I used to be one of the core developers of the system before I moved on to another job, but its still in active use by many sites.