I've been doing some hunting trying to find answers to many of these questions. Here is what I've found.
Most milksnakes that you are going to find in the pet trade are not pure. There are 25 or so of the Lampropeltis triangulum. The divisions after that are subspecies. So your Nelson's is probably a different locality with slightly different characteristics than say a Sinaloan, Pueblan, or Honduran. There are some general trends it seems, but because of the high degree of crossing between subspecies, its really hard to pin down a for sure length, behavior, width of bands, etc.
Nelson's if you can find a pure type, do tend to be a bit smaller. Many of these are actually Sinaloan x Nelson hybrids.
Your Honduran milk snakes will be longer, but again its hard to say how much longer. Many of these are crossed with L.t. polyzona. It seems as though Hondurans are capable of being one of the larger types.
A Sinaloan or Pueblan will be in the middle between Nelson's and Hondos.
I don't know much about behavioral traits. I've generally heard that proper handling over time can reduce their squirming. Milk snakes to tend to be flighty, as are kings.
Here are some links to info, and a link to a thread over at kingsnake.com that has a photo of a giant Hondo. I would ask those guys, they seem to know a lot.
Your right, Most milks no matter what ssp. are notorious for being flighty when small. They do calm down with age. If you are looking for "Pure" ssp. they are out there for both Nelsoni and Sinaloae. I actually work with a pair of each that can be traced back. Nelsoni usually stay around the 36" max mark and sinaloans can and usually reach 45" plus. Sinaloans also have larger red bands, usually averaging 9-16 where as nelsons have 13-18. There is an overlap on the red bands so you can always pick examples that are at either end. They both in my opinion are great animals as with all the other milks and kings. If I had to choose one for a first time milk keeper it will be sinaloan for sure. Good size, calm disposition, and brightly colored. Here's a hold back sinaloae in my collection.
My Two cents having raised Nelson's, Peublan's, and Hondurans
Nelson's seem to have a more wild tendency to me in all cases, but they calm down relatively fast, and over time loose that fidgity nature, but if they go a while without being handled, they will fall right back into the same routine of musking and running.
My pueblans are a joy to work with. Extremely docile and tame, they are nearing 3 years old and my male and females are currently 36" and have started breeding this season. When I first began raising them, they were docile and had no issues. Over time, they were handled a little bit less often than I wanted, and they became more wild, but again become quite docile soon after returnring to routine.
Hondurans . . . they have a bad rep to be honest. Mine exhibits a GREAT personality, and is so full of life compared to the others. The Nelson's was a dead snake compared to this guy. When I first got her, she was already tame and ready to grab without hesitation and would just chill in the handlers hands. Over a year later still working with her, she goes with me on all my education events. She's just over 5' and tamer than any other milk I've worked with. She has a comfortable girth so more people can feel better about having a grip on her.
If I were to do it over all again, I'd stick with the Pueblans to be honest, even though the Honduran works better for presentations, there is just somthing about a bright apricot Pueblan that makes it attractive. Good size, easy requirements, and tames fast. Even though I recently traded away my Nelson's to make room for more Pythons, I don't miss it too often. She was neat, but lacked a lot in personality.
Nelson's I raised
My Puebland Male 14 months ago
My female Honduran
7.6 Ball Pythons, 2.3 Carpet Pythons, 1.0 Green Tree Python, 4.5 Reticulated Pythons, 1.0 Burmese, 0.1 Woma, 2.3 Western Hognose, 1.1.2 Milk Snakes, 2.2 BCI