Hard to say under the new system, but I would still think Colorado and Palm Beach are still the premiere D3 programs for the same reasons they were before. Colorado is the only D3 program for 500 miles in any direction and the D2 conference in Colorado assures a high number of D2 recruits generated in your back yard every season. PBA is the only D3 school in Florida and again gets the luxury of having a lot of D2 recruits generated for which they have a distance/cost advantage. Some of those benefits may have eased under the new system, but I still think they make those attractive stops.
For D2, It is a little trickier as I think the "best advantages" are largely defined by locations where the low/mid major D1 programs are heavily Sim-owned and human competition in the locale is at distance. Having a D2 program in the Cal conference is a dream if only Cal/Stanford/USC/UCLA are human owned because there's a ton of D1 talent sitting there in your back yard. Ark/La./E. Texas have a lot of D1 programs generating recruits, but if the mid major programs are lacking humans, that can fall to a D2 in the region that then gets a distance and price advantage. A school like S. Indiana can benefit similarly if the Midwest mid-majors are coached by Simmy.