I've been through 4 zwave systems now. Every switch in the house is Zwave - about 70 modules, including a few locks, motions sensors, and stand-alone switch for decorative lighting. I started with the original Elk Zwave module, that turned out to have a fundamental design flaw with big networks and was discontinued (with no refund, or remedy I might add). Second system was HomeSeer 2 with a Homeseer Z-troller talking to the ELK. This was by far the most robust, even when using the elk as triggers for scenes - but there was a known bug with HS2 where it would corrupt the database in an unrecoverable way. I somehow got painted into a corner with a backup gone wrong one day, and ended up having to start from scratch. So I thought, I might as well try HS3. That was a journey of hardship. The zwave network would lock up, HS3 would crash or peg the CPU on the server. It was pretty much a weekly fix or reboot. I really didn't see any benefit to HS3, so I got pissed off one day and moved to ISY. For all my anger towards HomeSeer, they did know zwave better than anyone. The Z-troller had a battery, so you could run around the house add/removing devices, and then plug back in to sync. They also perform a nightly "defrag" on the network, and as a result, the entire system responded immediately (when HS was working)
ISY has a few issues, but is reliable overall.
1) You need a long ethernet cable and extension cord to move the unit around the house to add/remove nodes in the network. I don't understand what they were thinking....it's just infeasible to leave it in a closet somewhere and build out a network. I found that this was the only way to get it setup.
2) It supports maybe 70% of the devices out there. Homeseer seemed to go out of their way to update their system for special devices as they came out, ones that used extended features. ISY did not support 5 of my devices. A couple old switches, like the V1 circa 2005 kind, my HomeSeer multi-sensor/motion sensor, one of my original Z-wave locks, a fibaro rgbw controller (that can be used to control colored LED light strips), and a homeseer moisture sensor. That was 5 months ago, and ISY has not extended their Zwave functionality or device support since. I understand, they have to support a lot of things, and these devices are esoteric. But HomeSeer supported them just fine.
3) It's very slow. It takes about 5 minutes for my house to completely turn off all 60 lights, with a fully functional network (no missing/unresponsive devices). It gets a bit better after you "heal" the network, but you have to do that manually, not something that can run daily as a job. Any one device can take a few seconds to respond. Now a lot of this is just the general issue with how zwave works - if you have an older device, or a flakey device, or a dead device, it can screw everything up. HS seemed to be able to get around this somehow - mainly with it's nightly network re-discovery process I'd guess.
BUT, ISY always works - worst case it just takes a while. It's ELK integration is pretty good. It ended up being what I wanted, a totally embedded system - without OS and software stability BS I was experiencing with HS. But having said that, HS was more functional and higher performing, albeit much less reliable.
I am not sure how much it would buy you over a native Vera interface to the ELK. I really have not gained much with the ISY over the original native ELK zwave interface, but I hear there are issues with a VRC0P setup which is why I went with ISY (and I was a bit gun-shy from my original experience with elk's solution for lighting). Having seen ISY in action, and not needing Insteon support - I don't see any benefit if the VRC0P works well. The elk programming language is superior IMO - despite the ISY being a controller, it's basically a slave to the ELK used only for lighting control. While ISY can do IR, I find myself gravitating to roomie remote.
Oh, one last thing that ISY does well, that might be useful to you, is that you can send commands to it with http queries. Which means, load a URL and the ISY will do something - which is turning out be a good generic interface these days.
Hope this helps.