1. I would recommend you to start with Ocarina of Time because that seems to be a highly praised one. I need to get that this year. Another I would recommend the 2.5D A Link Between Worlds on the 3DS. It was my first ever Zelda and there were things I found challenging due to my lack of experience, BUT I managed to 100% it within 3 weeks. 
I also went ahead and beat Link's Awakening from 3DS VC, and bought The Minish Cap which I am about to start soon.
2. On Wii U, you would be able to play roughly half of them I believe. It has VC and Wii compatibility and Wii VC. However most handheld ones and GCN Four Swords won't be there.
3. I imagine Pro Controller would work for Wii U games, but Wiimote would be needed for Wii games/VC.
4. It depends on the Zelda game. ALBW is pretty short but amazing and lot's of non-story things to do. Link's Awakening was about 10hrs longer than ALBW for me, because I found it harder and there simply was far more to do between the dungeons.
Hope this helps. I'm new to the series and I basically simply went for it. I knew about the series since 2011 but always dismissed it until late 2013, and so I 100% guarantee you that whichever one you start with you will enjoy it a lot. 
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