hi sn1121, first difference is that the villas are at oppostite ends of the island.
leeward is on the east end, in a large neighbordhood of houses. i've never seen pelican's nest. the beach in this area is wide, there can be a bit of current/undertow. you would not be in walking distance to anything, but the drive to shops or grocery is about equal from either property. this area is very nice and quiet.
limbo is near turtle cove marina. you'd be in walking distance of 5 restaurants and a dive shop. i know for sure that the walk to the beach is 3 minutes. you will walk a 100 yards down a Very quiet street, then down a short beach path. you'll come onto the beach next to bella sur mer. if you look at the 6th photo from this page it shows the beach you'd be using: http://www.bellasurmer.com/#
also limbo is in walking distance to one of the 2 off beach snorkel areas on provo. >smith's reef which would be a 10-15 min walk down the beach from limbo.
this map might be useful: http://www.aquamarinebeachhouses.com/map.htm
bella is a wonderful house if it's available. has nice pool - fun for little ones and perhaps a bit safer set up for kids.

provo is very laid back like st. john but not lush and hilly and with more a much better restaurants.
also with pelican it will be about a 40 min drive from airport to house. for limbo about 20 mins.

fyi - you might think of taking things like cereal for kids, pb&j, mac & cheese, tuna, coffee/tea in your suitcase. saves only a little money but ensures they get the kind they'll eat.

another proprety you could look at the stay in is the aqua marine beach houses. if you click on the map instead of scrolling you'll find it. this is mid island and several fodorites have stayed there and were very happy.

I have not been to Limbo, but I've been to other properties managed by TCVillas, and they are impecable. Gorgeous, well maintained, nice properties, so I can only assume Limbo is nice. It's around Turtle Cove area, close to restaurants and excursions, great snorkeling from the beach-a little rocky for swimming though.

I have been through Pelicans Nest, it's stunning. It sits back from the beach, so it insures privacy, but they own the land in front, so you still have ocean views. It has a huge kitchen, open floor plan, and is updated with everything you could need. The decor is gorgeous. It's in a quiet residential area, chances are the beachfront will be all yours-and you can walk the beach all the way down Grace Bay.

I love St. John, been about 3-4 times. T&C is completely different. T&C is flat dry and scrubby, but has blinding white sand and neon turquoise water for as far as the eyes can see. St. John has awesome scenery but more people, T&C is about the beach and water. I find the restaurants in T&C to be much better too. T&C is laid back and quiet.