I have the choice between:
I have read somewhere by a GPS manufacturer that antenna size is more important than efficiency but I feel doubtful about that. Would like to hear your thoughts.
In principle bigger is better but we are talking about a GHz signal here (I don't remember the exact frequency); since we are not talking about short antennas (in the electrical sense) I think that matching and a proper lobe would be more important than raw size.
I guess that being bigger should have a slightly better gain
Everything else being equal (same type of antenna, same gain...), a 35x35 mm antenna should receive nearly twice the power compared to a 25x25 mm antenna. That means that even if the smaller one is slightly more efficient, the larger one still results in a much higher output power.
But there are lots of other parameters that may affect the performance of antennas. Your best bet is to test both antennas in the same conditions (preferably in a wide set of conditions) to see which one actually performs best (in each case, possibly).
Of course, beyond the performance of the antenna, there may be other considerations such as overall size, cost, ease of integration, etc. As noted in your quote, the measurements are based on the use of a pretty large ground plane, which may or may not fit in your application, for instance.
