Kilts are great to hike in. I hiked in my Mountain Hardwear from Neels Gap to Katahdin. I still hike in it...although this last trip, it failed miserably on the chafing problem, so I might buy a new one. I also have a sport kilt, but it is heavier than my other so I haven't taken it for a hike yet.
With all that said there are great advantages to kilts. Obviously the do help reduce chafing. And if you have to "do your business" it is extremely easy. You can also change clothes in front of anyone, just pretend its a towel.....
I never wear anything under my kilt unless I am in camp...then I might put a pair of boxers on to avoid flashing everyone my "dirty bubble gum".
Yes, you do get some funny looks in town, but they already think your crazy for hiking 2000 miles so who cares?
Wear a kilt...its a good icebreaker if nothing else.
oh yeah, as for it getting a bit nippy....that's why you carry extra socks!