Suvid, I’ve thru-hiked the Smokies in March and in August. You will need to get a permit from the park service. You can reserve the shelter up to a month in advance. You’re required to stay at shelters, but you could probably get away with ‘stealth camping’ if needed.
I found the hike from Fontana - Newfound Gap to be a bit more difficult, yet rewarding. Newfound Gap - Davenport Gap is easier as your’re walking a ridgeline. At many points the trail becomes very flat.
It’s no problem hiking alone in the GSMNP. You will find, even in June many people up there hiking. When I was there in August there were several thru-hikers I was hiking along with.
The weather is always unpredictible in the GSMNP. I have no idea if it will be muddy or dry. You shouldn’t have any problems with bugs at that elevation. And like I said, you won’t be alone. But it shouldn’t be overly crowded.
I’m actually planning on hiking from Fontana - Climgmans Dome sometime in April. April 1 is when Clingmans Dome road opens again.
Go with either side of the park, you can’t go wrong.
Here’s a link to a nice site which provides a trail map of the GSMNP.
http://www.nps.gov/grsm/pphtml/maps.html
guru