I recently finished the game, too. Excellent story.
1. Remember, the story deals with the future affecting the past. I don't understand it completely, but I think it's got has something to do with it. It would explain why Sigma didn't know about the mechanical arms even though they've seemingly been there for a long time.
2. That's never fully explained, ut I believe that it's possible something might've happened to Clover in the future that made getting an older version of her impossible. Therefore when they had the chance to grab her with Alice they just found that to be more convenient.
3. If you get the secret ending, obtained by getting all of the gold files, it absolutely screams 'sequel time.' And since they never fully explained what happened at the facility to cause Radical-6 (or what necessitated the mechanical arms), I'd say a third game is inevitable. Not to mention that we really learned barely anything about Phi, when you think about it.
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