Hi MarcoGT,

in our last trip with baby through FRA we were given luggage tags for both parts of the stroller at check in and then drove it to the gate in VIE.
In FRA they returned it from the cargo hold to the gate area; this took a while, however. Maybe not optimal for short connections.

Onward flight the same, but at final destination (ABZ) the stroller was delivered with luggage. So it seems to depend on station.

Hope this helps.
David

Edit: you may want to give it a try to check you and your wife in with a seat left in the middle (if flights are 3-3). We were lucky enough that the middle seat stayed empty. Chances are higher for a middle-seat to stay empty than window or aisle.