I thought I loved him when he went away; I love him now in another degree: he is more my own.Why so? When he is away and will die (or is dead). Why is he more her own when they are not together and will never be? She loved him when he departed, because he gave her a school, respected her need for individuality and loved her for herself. These are very good reasons to love him but it doesn't explain why she should be happier without him. We can't really infer everything from the text, so we must consider Charlotte Brontë's own life. The key is, Paul respected Lucy's need to be an individual. While he was with her, he did admonish her and try to convert her at first. Now he is gone, she can breathe and be her own person. A strange way to love someone, but not unthinkable. Charlotte was an eccentric after all. Of course Lucy liked to be left alone in the art gallery, instead of walking round with John Bretton. Absence does make the heart grow fonder, particularly when the object becomes unattainable. Still, why is he more her own?
Remember M. Paul likes to talk and discuss, may well have enjoyed the company of other people (so Lucy may have feared, preferred their conversation to hers). With him gone, she doesn't have to share him with those people, especially the nasty Catholics who tried to convert her. On second thoughts this sounds mildly ridiculous. With more time to write to each other, of course they know each other better, and so he is of course more her own. "In another degree" - this however points to another reason as to why she loves him more.
When Lucy says "he is more my own," does she merely mean she owns him and his love now, or does she mean something else? As in "he is more of my own kind"? Charlotte liked to talk about people being of each other's kindred - only see Jane Eyre of Rochester, Caroline of Robert Moore. Frances Henri in The Professor says people love each other better when they suffer together. This may not be strictly true, but the sentiments may be mirrored in Villette. Before sailing, Paul has not suffered as Lucy suffered. He has relations and friends and more financial stability than her. (He could rent and furnish a building for her school). He is also respected. He has also loved successfully to an extent - he was supposed to marry a girl, but she became a nun and died. She did however love him in return, though Graham didn't love Lucy. When Paul goes away, he is facing new troubles. He has just escaped the attempts of Madame Beck to part him and his love, Lucy, and he will be parted from Lucy for some years in a strange land. Just as Lucy was forced to leave England to seek a living abroad, alone and friendless. His relations turn out to be schemers and therefore contemptible; Lucy has no friends apart from the Brettons and the de Bassompierres (and she is not fully part of them either). Both families are English, which shows you her friendships are limited to her countrymen. With Paul gone he will have suffered the same problems as Lucy, and now they can understand each other better. Instead of mere pity, it is true sympathy and shared troubles that unite them.
ksotikoula wrote a very interesting discussion on her blog on the subject. She says it means Lucy doesn't need M. Paul's physical presence to be happy, she is just happy mentally and emotionally. The Ideal of the person was more important than his actual presence. Ksotikoula's instinct is acute when it comes to Charlotte Brontë. This love is much greater than his actual presence, and it makes Paul more Lucy's own, because she can imagine what happens between them and immortalise it in a book - Villette, that is. Instead of harping on the reality, he belongs in her imagination, where she can picture their happy reunion.