My biggest knocks against footholds used in classic pole sets is that:
1) I don't think the sets hold up as well in super heavy snow areas. This isn't a problem if it puts sets out of commission once or twice a season, but if it is every single check its no good. I might have a tendency to use too big of poles though. (I started wondering about this some years after rejecting poles.)
2) Cutting or coming up with poles can be a lot harder than you would think in certain terrain. Funny as this sounds, it is very very applicable in some places.
3) They are at least somewhat more prone to birds.
Those are the only reasons I don't use them. I definitely believe that they have less refusals and will catch marten that will walk by a plant pot vertically on a tree. I am seriously considering running poles to my plant pots, but then you have some of the same issues as above and am unsure if it is worth the time and effort. It is complicated by the fact that there is so much snow on our line that you often don't get good opportunities to see marten tracks and observe set behaviour. I have not used footholds in boxes except on the ground targeting mink. (Have caught marten in them of course, but don't like ground caught marten for all the normal reasons although in my area rodents chewing on critters is not much of a problem, snow burying ground sets much bigger problem.)
Obligatory, this is my opinion for my area.

I would love to run horizontal boxes with poles seems like a lot of the advantages of both. How snow resistant and bird resistant do people find these? (Although at this point I might still run plant pots because I have set them thousands of times and am very used to them and my system is set up for that.)