The Stilo with the biggest gearbox appetite is the 1.6, but it's a pig of an engine as well, with an unreasonable number of examples suffering engine electronic problems. Therefore you're better off without it, even though it's one of the most common models of the Stilo range (probably why the Stilo got a reputation for being unreliable).
The 1.2 gearbox is a 6 speed and is better, but not perfect. Failures have been reported but not as many as on the 1.6. The 1.2 engine is a lot better too.
The other engines/gearboxes are fine & don't seem to have problems (save for the 2.4 needing attentive maintenance) but if you're only doing small mileage the choices (1.4, 1.8, 2.4 petrol & 1.9 JTD) are probably not ideal, with the exception of the 1.4 which would be OK.
Have you thought about a Panda? These can be picked up from under £2000 now and the engines & gearboxes are no bother at all. As a Stilo owner it's fair to say that much of the electrical faults are often just a duff battery rather than actual electrical faults, but the Panda is altogether a more reliable car. The only fly in the ointment on a Panda is the Delphi power steering motor (which the Stilo doesn't have) but these don't seem to fail as often as on the Punto.
