There definitely certain things that are not covered today by host profiles, some others that I've heard are iSCSI configurations and duplex configurations on your NICs. I guess we can add jumbo frames to the mix as well ... though you can definitely write up a vCLI/PowerCLI script to update it but yea it's a pain that it doesn't cover all params. Might be worth mentioning in an SR ticket to VMware
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VMware ESX/ESXi scripts and resources at: http://engineering.ucsb.edu/~duonglt/vmware/
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We hit the same issues today. We'd already configured everything for jumbo frames and found that a few other settings were different, so we thought we'd get host profiles to apply them all. Trouble was it also recreated the vswitch configs (even though they were already identical) and in doing so dropped all out MTU 9000 configs out.
Gotta love it