A few issues with bubblers -

1. They're extremely hard to clean. I can't even count how many stories i've heard of people trying to clean their downstems and end up breaking it.
2. If it's a hammer and not a sherlock, you are most likely going to get dirty water in your mouth at some point.
3. Bongs are just better. Even a small 6-7" bong is much better than having a bubbler, especially if it's not going to leave your house. IMO having a nice bong at home and smoking blunts while out at parties and the like is much better than having a bubbler.
4. Emptying out the bowl can be a pain because the bowl and downstem part of the bubbler are not detachable, so you might end up with wet weed or a wet bowl.