Before I go into the rabbit hole. My MIC system is connected to an Avaya CS2100 via 2 Dialogic Gateways. We are about to pilot a Cisco UCM and they want to connect it to the MIC system as well. First, is this even doable? I don't want to route calls back thru the Avaya, I'd much rather just direct SIP trunk from the CUCM to the MIC. Can you segregate traffic like this?

You can add as many SIP lines as you need to MIC. Also yes MIC supports communicating to cucm. This is no different then how we talk to the DMGs.

Bear with me....new to MIC (it's changed a lot since 2.3.1 which we had been running). Will it be able to use the SIP trunk to the CUCM for MWI?

Yes, but to support two different MWI targets, you need to specify the full MWI URI for the CUCM users. (1234@10.0.0.1) instead of just the MWI extension of 1234, for example. You can also do this with a handler customization if the extension is enough to let you logically decide where to send the request. I forget the exact handler name, but if you use Designer's Dependency Viewer to find handlers using the Set Visual Indicator tool step, there should be only one.

FYI, this is working. The main thing on the CUCM side is to make sure the Calling Search Space (CSS) for INBOUND calls on the Trunk is set for the CSS the voicemail is using.