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My suggestion:

A Pro controller

Tempered glass screen cover. They're very inexpensive.
http://m.ebay.com/sch/i.html?_from=R40&_trksid=p2334524.m4084.l1312.R2.TR12.TRC2.A0.H0.Xswitch+.TRS2&_nkw=switch+tempered+glass&_sacat=0

A hard shell case is something nice to have.
http://m.ebay.com/itm/Hard-Shell-Carrying-Case-EVA-Storage-Bag-Cover-Protector-For-Nintendo-Switch-/282391603017?_trkparms=aid%253D222007%2526algo%253DSIC.MBE%2526ao%253D1%2526asc%253D20150519202348%2526meid%253Ddd986411f67342039bf684546feb9e7d%2526pid%253D100408%2526rk%253D4%2526rkt%253D23%2526sd%253D232303056587&_trksid=p2056116.c100408.m2460

As far as the JoyCons, they do charge while the system is off. You can't charge them with the comfort grip. But the battery life is 20 hours. I've never had to stop playing because of charging.