I transitioned to ESXi.
Of the things you mention, only mbralign won't work on ESXi, as it doesn't have a 'full' console.
You could use a Linux machine to run the mbralign tool: mount the VM NFS share, and run the mbralign utility on Linux (make sure VM's are off).
With ESXi 4.1, VMware added an option to enable "Remote tech support", this enables SSH !.
(You could also look into vMA or ESX Powershell)
So you can enable SSH, and use your favorite cli commands, like esxcfg-vswitch and such.
Jumbo frames aren't enabled by default (still mtu of 1500), so you would have to do this by hand, like you did before.
A reason for staying with ESX would be specific (hardware) agents which can't be installed on ESXi.
Regards,
Niek