Hello everyone!
First of all thanks to all developers for making this awesome idea happen!
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My Questions,
With skywind, is it possible to fast travel from skyrim to morrowind with my existing level 30 character and start the main quest over there with quests from skyrim activated etc ?
I use a skill mod wich uncaps the perks(for example my one handed damage perk goes up to 16/16 instead of 5/5) plus the maximum skill level(goes above 100).. Is that a problem? Does skywind uses its own skill system ?
Thanks! :)

Fast travel is possible to
Fast travel is possible to Vvardenfell is possible:
Use the map marker plugin or use the console (cow wrldMorrowind -5,-5 to be teleported to Balmora)
http://morroblivion.com/forums/skyrim/skywind-mod-releases/5650
Since we didn't release a compatibility plugin you would have to use the console commands to start the main quest. You should be able to start the other questlines already completed (mages, etc..)
With regards to skills, all is vanilla (skills and perks), so there shouldn't be any issue.