I tried playing with link aggregation recently (i do not have Cisco and used asus rt-ac66 router for experiments) and paused for a while.
my findings are:
- probably there is no need to do bonding on virtual part (at least from the very beginning) as vmxnet3 driver is quite capable by itself - http://www.vmware.com/pdf/vsp_4_vmxnet3_perf.pdf
- my jetway board has Intel's 82579lm and 82574l NICs (both are currently supported with ESXi 6, though with 5.5 i used community drivers). 82579lm is also used by Intel AMT which in turn used shared (with the host system) MAC of that NIC
- ESXi management network is using 82574l MAC and this NIC is the first in failover order for mgmt network, while another one is the first for vM network
- after enabling LACP (used VDS on ESXi side), on both sides, from roter's side I noticed that partner (ESXi side) was using 82579lm MAC (where AMT is) and I could not force it to use 82574l MAC and that lead to inability of ESXi host access
at that point I paused for a while, to find out how can I switsh from shared MAC for AMT to a dedicated one. Per intel AMT documentation this is possible (in theory???)
May be you are facing the same thing - bonded link is using MAC which is not the one used by mgmt network, so its MAC is not exposed and cannot get IP?