Alitalia has a history of unhappy and uneasy partnerships. I remember one with KLM, a good while before Skyteam was created, that suddenly from one day to the next went pear-shaped. I think an Alitalia and Air Berlin pairing would be awkward and uncomfortable at best.
To be honest, a couple of years ago I thought Lufthansa was repeating the Qualiflyer mistakes, having taken over a raft of loss-making airlines (Austrian, bmi, Croatian, etc.). But the tide seems to be turning.
To me, Air Berlin doesn't feel very much like a LCC when I fly within Europe. A sort of full service is provided (granted, if you want more than the basics you have to pay for it) and I've never had to pay for a bag (unlike the fiasco I had at Iberia recently). I would be very sorry to see them go. I think they provide some much needed competition to Lufthansa, and, frankly, a better in some ways.