Depends on your particular goals, if this is an indoor strain tight internode spacing and squat structure lead to higher yields and less concern about plant height or growing 6ft worth of lanky sativa for 4 oz where you could have had a 3fttall indica yield upwards of 12 oz but if growing outdoors in a tropical climate a lanky sativa with loose buds will yield where a super dense indica may get botrytis early on and ruin your whole plant, so basically boils down to personal preference, if you like the short one keep it if not scrap it but you can only judge 1/2 the plants traits without flowering who knows maybe the short one will stretch ridiculous and the tall one not move an inch, guess well just have to see right?