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The main difference is that VERA 3 has an integrated Wi-Fi Router and has twice as much memory (128MB) as the VERA Lite (64MB), it also has two USB slots.
This is a fairly obvious one. VERA3 includes a Wi-Fi router which includes four Ethernet ports and an ADSL/Broadband port. This means that VERA3 can be used as the main Wi-Fi router if you don't already have one installed or as a secondary router if you wish to extend your home's Wi-Fi coverage. If you don't need any of these then VERA Lite may be the better solution for you.
One of the benefits of VERA3's extra memory is that it will generally operate faster than VERA Lite. This is especially true the more devices you have on your network and if you are running plugins. The extra memory gives more 'head-room' to the system, enabling tasks to run faster.
Each device you add to the system needs its own memory, so the more devices you have, the more memory used. Typically each Z-Wave device uses around 0.5MB of memory, this means the VERA Lite can run up to 75 devices, whereas the VERA3 can support up to 200 devices. VERA3's extra memory also means you can run more plugins.
The VERA3 has two USB slots, which means you could have a USB stick collecting log data as well as another device such as the RFXtrx433 transceiver. This isn't essential, but does give you more options.