I think you have to view this in the context of the wider squad. Likely in the next 2-3 years we'll be seeing the back of Milner, Keita, Henderson and Chamberlain at least. Thiago probably not long after. The much-discussed 'midfield rebuild' still needs squad players, which is where Jones is right now. Homegrown, experienced in the system, with a capability to improve, signing him up long term while we construct the next generation, which he'll more than likely be a part of, in midfield seems to make a lot of sense.