is there a speed difference between the two, i.e. are you at a disadvantage if you use one versus the other? what are the main differences in terms of functionality/features?
Huge difference. WebTrader is meant to be a stopgap for people that can't run TWS, and need to place an order or see what's going on. It has limited products, order types, data, etc. Speed disadvantage comes primarily from the nature of having to fill out and submit a web form instead of the click/hotkey nature of TWS.