Potentially, yes. Lithium batteries do not like being stored full, and they do not like being stored empty. Improper storage can potentially impact their longevity - presumably, Apple batteries have built in protection circuits designed to try to avoid such a scenario, where a protection circuit can cut off power-on ability below a set voltage (but above the threshold voltage where the battery goes into a sleep mode that a standard charger is unable to awaken it from.) If that is the case, the likely reason it took so long for the system to power on could be that, even though it was charging, its voltage was still below the minimum voltage required to allow a power-on.
Is the battery running well? By that, I mean what kind of run times are you getting?
Are you going to get AC+ on this system?