Part of the problem is Ibanez has a reputation as being the "Walmart" (I've heard this more than once) of guitars and basses. They've saturated the market with instruments for everyone - from the kid, to the beginner, to the garage warrior, to the discerning professional, to your Grandmother......they're all branded "Ibanez".
Fender made the delineation with Squier, Warwick with Rockbass, EBMM with Sterling, Gibson with Epiphone, sure Yamaha brands all their basses "Yamaha" but they don't have the variety and number of almost overwhelming choices that Ibanez have had over the years. It's a very unfair reputation, they make terrific basses at reasonable prices at all levels, go up to the prestige and premium levels and they can hang with other boutique basses.
Never thought about the branding before, but now that you've mentioned it I can definitely see where it has probably hurt them.