I prefer
Susanna. I like the name. I think it's a step up from being boring and too dated because it has a certain charm, but it's not a favourite. I think it would be really cute to see on a little girl, but I probably wouldn't use it myself.
Hard to say with nicknames... I think
Susie is more likely to happen than
Sue, without you encouraging either. If you always use the full form, most others are likely to as well, and it's also likely the child would end up preferring the full form too, but you never know.
I think
Lily and
Susanna are fine as sisters :) The names don't sound alike and most people aren't super into looking up meanings of names (or they're bad at it anyway and use poor sources).
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The human brain is a haphazard, messy machine that glitches at the slightest, strangest provocation.