Here is a breakdown of their differences:
Traders will need to use one of the helper programs mentioned on the site. Whichever program you choose, you would need to have it running on your computer and your computer needs to be ON for AutoTrading to happen. All Gen1 accounts are read-write which means traders can enter manual trades. Since AutoSync is a manual setting controlled by the trader, a manual trade will not disable AutoSync like in Gen3. Prices vary so check program provide for current prices. A steady internet (24/7) is the most important thing to consider.
Open positions are managed via the helper software and will not be visible on the C2 Open Positions page.
No software to download and your computer can be off for trading to happen. All of the brokerage firms and introducing brokers on the C2 website offer Gen3 technology. AutoTrading fees associated with Gen3 are listed here: http://www.collective2.com/prices
Ultimately the choice is yours. Feel free to check out the C2 forums to gather feedback from other traders if you want to perhaps get their take on the two different technologies.