Sunny? Sounds just like Sonny Boy.
Indigo. Possibly suitable if you live in a yurt and sage smudge your babies to prevent Diptheria and Measles. She'll just as likely change her name to something like Elizabeth or Sheila just to piss you off, though.
If you like Tilly, you could go for Matilda and only have 2 of them in each class, rather than be one of the 5 - 8 Ottilies.
Tiger is likely to be changed into Tigger or Tiggy. Not bad if you're planning on her becoming a Nanny to the Royal Family, I suppose. Or a hedgehog.
Clover is a brand of margarine. so she could be called Marge.
Margaret/Marguerite/a gets you that as well, along with Mags, Maggie, Moggie, Meg, Peg and Madge.
Clementine. Calling the register in a couple of years is going to sound like a shopping list.
Juniper. Yeah, more shopping - it's the essential ingredient in gin. If she's due in five months, you might just slip into being able to call her Junie without people saying 'but she was born in April/May'. But she'll be constantly saying 'No, not Julie. Ju-nee'.
Mollie. Fine. I always liked Millie Molly Mandy books when I was little. Even though even that kid had the full name Millicent Margaret Amanda.