Shorties - Can retain midpipe, ie you can put the cats on if need be, will have ZERO clearance issues, can install and remove tranny just as if they weren't there. May or maynot pick up power. I gained 20rwhp with FRPP shorties.
Mid's - Limited selection of mid pipes, limited selection of headers, USUALLY no clearance issues.
LT's - Usually highest rwhp gain, some clear for tranny removal, but not all, decent selection of midpipes and headers available. Some people have clearance issues, ie speed bumps, driveways etc, however I know at least 2 people on lowered suspension cars with them that have had no issues.