Yes, theoretically, given an equal cylinder volume, a 2 stoke engine will be more powerful than a 4 stroke. Practically, to take advantage of this extra power, the 2-stoke engine needs to be working in a much narrower and higher range of engine RPM (rounds per minute).
If speaking of motorcycles or scooters, a motorcycle typically will need to do a lot of extra gear shifting in order to make a good use of this power. On scooters, which usually have automatic or CVT type of gear shifting, the extra power will be less noticeable.
2 stroke engines offer other advantages that make them good candidates for small motorcycles and scooters. They are lighter, smaller, simpler and usually cheaper. Disadvantages include being more noisy, have higher fuel consumption and more polluting.
Back to your question, a 4-stroke 125cc scooter will be more powerful and more pleasant to ride on than 50cc scooter (or 125cc 2-stroke scooter for that matter, although the 2-stroke 125cc will have more raw power).