Storm wins against Sue for a number of reasons.
1) She has extremely fast reaction speeds.
Here are some scans:
http://img122.imageshack.us/my.php?image=energyworld42xc.jpg
http://img152.imageshack.us/my.php?image=energyworld57hb.jpg
Notice, the caption states in plain english that this gives her an advantage in any fight. Her reaction speed is definately above normal people. Sue counts as normal.
2) She doesn't have to start her lightning bolt from the sky. She can start it right on Sue. She's created thunderstorms right in the palm of her hand as shown here:
http://img367.imageshack.us/my.php?image=smallthunderstorm2cq3.jpg
So her bolt can start right on Sue at the beginning of the fight and knock Sue out. In order for Sue to put a force-field inside of Storm, she has to project her energies from herself into Ororo. Storm's attack starts right on Sue and she has faster reaction times.
3) Storm can work her powers through Sue's force-field therefore, Sue has no real defense against Storm's powers. We see her doing that here:
http://img190.imagevenue.com/img.php?image=66129_Uncanny_X-Men_Annual_405_Page_33_122_184lo.jpg
http://img180.imagevenue.com/img.php?image=66136_Uncanny_X-Men_Annual_905_Page_34_122_101lo.jpg
She was inside Sue's force-field and controlled the weather on the other side of it. She would be able to do the reverse since they are the same thing. The force-field's interior is composed of the same energies as its exterior. Hence, Sue is able to not only block out explosions, punches, and energy blasts by putting a force-field around herself, she is also able to contain these things by putting a force-field around what she wants to contain.