HyperLynx PI uses full-wave planar solvers which generally means that you need plane cavities but we can model traces for cap mounting and pin connections. We're working on some additional solvers to handle cases where the whole circuit is traces. I could discuss this more off line with you (you can email me at steven_mckinney at mentor.com).
On the VRM question, probably best to get an SR entered for this. Generally, if you have a series inductor, it's because you're trying to provide isolation beyond DC or a few KHz. Therefore, the section of the design that the VRM is on, really doesn't play into the AC behavior because they are electrically isolated. If you are seeing high impedances in the low frequency range of your extraction and want to bring this down, one work around might be to place the VRM at the pin of the inductor on the plane so that your capturing the low frequency behavior of having something there....but again, I would run this through the support guys, I'm sure they've handled this with other cusotmers in the past and might have a better recommendation than me.
Thanks Steven, I have sent an email to you so hopefully we can discuss the issue further.
I was also wondering if Mentor plan to include PI support for multiboard analysis at some point?
It is part of our plans to support multiboard in the future but it's a large scale project so I can't give any exact timelines at this time.