I have a special spot for 3rd simply on the basis that it was my introduction to Ars Magica. Third Edition added unnecessary changes True Reason and and also tried tying the setting to the World of Darkness and the Tremere. It is my understanding that changes were dropped beginning with Fourth Edition. However, despite the special spot I have for 3rd, I would go with 2nd or 5th.
I have never owned or played either second or fifth. but the following is based on my recollection from message boards. Second edition, is a lighter game, "Mythic Europe" was not fully fleshed out and the game's indie roots show. As for Fifth edition, people on rpg.net and other sites tell people that, if they are considering fourth or fifth edition, fifth edition is the way to go. Fifth from my understanding is a cleaned up version of fourth that also fixes issues with fourth edition. Furthermore, Fifth Edition, like other post 2e editions, is more complex, crunchier, and "Mythic Europe" has been fleshed out into a full setting with a lot of support.