Yes, I've used the System Three waterborne primer, though this is a bit of a misnomer. It's water clean up, but is still a petroleum base product. The addition of an emulsifier, permits water clean up, though you do have to scrub pretty good, nothing like the acrylics. This particular primer will cure hard as stone, in spite of water. I had a tray of primer that I intended to clean out, but didn't have time when I put it down. I figured I'll just drop the whole thing in a 5 gallon bucket of water and would get back to it after I finished up. Well I forgot about it and a few days later pulled the tray out of the bucket, to find the primer was completely cured.
The System Three stuff works well, but you do need to sand it within 3 days of application or it becomes much harder to do.
I too use acrylic urethanes, but much research needs to be employed for the application as the polyurethanes and acrylic urethanes have distinct advantages and disadvantages. Solids content tends to be higher on the polyurethanes, but these also are a bit harder for the backyard builder to work with. The acrylics tend to be thinner and much more clear, but also cost more. the percentage of urethane to acrylic can be a factor as well, particularly if you need something more rigid or more flexible. Lastly the naturally lower VOC levels in the acrylics has an appeal to some.
In the end, it's really experimentation and comfort level. This will be based on shop conditions, skill and equipment levels too. I'm using some industrial, some automotive and some marine finishes. I use epoxy primers regardless of top coat, just because I've been screwed too many times in the past. Interestingly enough (at least in my case), the better you get at applying a finish, the more costly and difficult to apply these finish products seem to become. Damnit . . .