Wow a topic on something I was thinking about yesterday. However, in my case it isn't for traveling, but for storage. The trailer I got spec'd out at 10'4" tall, but after measuring it, it is actually 1-'8" tall. Apparently there is a discrepancy in the AC unit, it is 15" tall. My barn is exactly 10'8" floor to truss, so I need to lower my trailer about 2" to safely get it inside during off season.
I was considering buying a set of 4 12" wheel/tire combos, which should give me the clearance needed to get it inside. That and it saves the road tires from sitting all winter with weight on them. Since it will never be on the road with the 12" tires, not concerned at all about weight in this case, but the only thing I do need to be careful of is that nothing underneath can get damaged when backing in or pulling it out. It would also have to go in perfectly level and there is a small rise where the slab meets the apron at the door that I have to be watchful of, but other than that, I think my plan will work.
As far as lowering one for transport, I don't think that is such a good idea, they hang pretty low underneath to start with. I don't think putting smaller wheels on would help any, but may cause other issues like heated bearings. As mentioned by another poster, if the rig is setup correctly, there should be minimal issues while towing. If you are having issues with a proper setup, it could be you don't have enough TV for the trailer. The bigger the trailer the more TV you need. The trailer I got is at the limit for my truck, when fully loaded it would put it at just under 14K# which is the rating of my truck, but I doubt it would ever see a full load, that would mean I forgot to drain the holding tanks. EWWW. Been there, done that, can't smell pine spray the same way ever again.