Mark,
The issue is that while internally it is a 5Hz GPS, it doesn't send GPS out at 5Hz, only at 1Hz. So all SkyView sees is an update at 1Hz, even though the GTN is faster inside. It was never designed to be a "GPS position source" for other equipment in the plane. The 430W was a 5Hz GPS as well and had the same output rate issues.
Just because SkyView is using the position from the GTN doesn't make SkyView certified. A certified GPS means the position sensor, all the software, and the databases are all certified. The GTN is your primary navigator, and you must be looking at that when in IFR. You can use the CDI on SkyView because that is displaying a direct command from the GTN, but not the map portion of SkyView, since all the databases and such come from our own certified equipment. Thus, it really doesn't matter which GPS position sensor SkyView is using in IFR. You are legal by having the GTN, as long as you use the GTN itself as your primary navigation.
In the end, if you feel more comfortable with the GTN as your primary position source, that is supported as I mentioned. We just very much believe that your experience will be better with the SV-GPS-250 as your primary. Either way, one of the awesome and unique things about SkyView vs. other experimental GPS units is that we do support multiple GPS inputs and can fail over automatically. We even give you a warning if a position source fails.
We've had a lot of experience with all of this integration and the ins and outs of IFR requirements in an experimental (I have a GTN in my personal plane), so let us know if there is anything else we can do. There's a lot going on here!