I've been working on my swimming since late spring of this year. I have also done some water aerobics. Here are my thoughts:
1. It's true that I see a fair number of people who are in the pool doing their exercise are there because it is the better modality for physical limitations/aggravations (this includes me). But I couldn't say that the pool is filled 100% with people who could/should be doing a different workout. I don't think that is true.
2. There isn't any evidence that water aerobics isn't inherently aerobic. Someone wanting to expand their cardiovascular system has the opportunity in class to do so. I found it to be aerobic. I also found those pool weights to shred the arms.
3. One of the things I have noticed about people and their workouts is that there is a tendency to hear a need for a workout as a chance to give suggestions based on preferences and not actual data. A runner has always recommended running. A cross fitter always recommends cross fit. Cyclists/spin people always recommend a bike. Before my injury? I recommended videos!
I think it's possible your doctor is recommending what works for them. It also may be that a bike is better for building muscle and bone in the lower body compared to the water but they weren't able to communicate that in such a way so that you could think critically about a)whether that is a concern for you and b) if so what activities could fit the bill.
4. Swimming in particular has a skill/technique based component to it in order to reap the rewards. I started out as a beginner and probably will be a beginner for the next year or so. I am now able to complete 900 yards freestyle in 30 minutes. This is a great improvement for me! But when I put that effort into a calorie calculator, I might as well have just gone for a leisurely stroll. There will have to be more effort on my part to burn calories and build muscle with swimming. And I need more coaching. So it may be that your doctor has seen people in the pool not expending enough effort to get results.
5. I think I need to add weight training back to my weekly routines. I don't think that (even consistent) pool exercise is enough for muscle building/maintenance. When i say weight training, I really mean Margaret Richard.
Curious what your thoughts are to my soapbox here.