It's pretty easy to convert any e-bike to Li-Ion. If you're considering new bike entirely, you might consider an IZIP. If you go with one of their lower-end models with SLA (ie:
IZIP Trailz AL,
IZIP Mountain Trailz, etc.) you'll have the option to upgrade to Li-Ion next year. Currie is creating a new Li-Ion battery pack which will fit into the existing rack-mount design in 2009. So if you want to upgrade... it's as easy as buying a new battery and plugging it in.
About the batteries... you actually want to do the opposite (if possible): don't ever let SLA batteries run all the way down. Try to keep SLAs topped off whenever you're not riding and always re-charge directly after use.