The capacity of the NiMH batteries is certainly a factor in determining how long they can power the scooter, but does not answer directly why the scooter runs poorly (i.e., "barely moves") for even a short time. Another characteristic of batteries is how fast they can discharge, i.e., how much current can they provide. Large lead acid batteries can provide very high currents -- enough to weld with even. Some other battery chemistries can do the same, such as LiPo and NiCd. NiMH are less capable in general. Note: some variations on NiMH batteries provide greater discharge ability than others.
Discharge rate is often stated as a multiple of the capacity. Thus, a battery with a capacity of 3000 mAH might have a discharge rating of 1C or 3A or it might have a rating of 30C or 90A. That rating would determine how fast your scooter would be able to go with the new batteries. For more on the subject, see: **broken link removed**
You can increase rating by putting the batteries in parallel. In this case, if you had 64 batteries, you could make four strings of 16 batteries each and put them in parallel. That would improve the current capacity, but performance may still not equal the lead-acid battery.
John