CompactLogix has less logical and physical capacity for EtherNet/IP I/O connections, but it can run anything* the ControlLogix can as I/O objects.
See the CompactLogix Selection Guide and the "EtherNet/IP Modules in Logix 5000 Control Systems" (ENET-UM001) manuals for details about Ethernet packets/second and CIP connection capacity.
* Except motion control over CIP Sync. That's a ControlLogix feature using the 1756-EN2T and -EN3T modules.
No worries, I do this all the time. Like the Ken said, just watch your connections. We first outgrew the L34 (and then they killed it), so the L35E was the logical progression. Never any issues combining Compact and Flex I/O.