Tuff choice. I used to own both a small glass bubbler, and a 1 foot glass bong.
The bong undoubtedly gave the smoother hits. Dont get me wrong, the bubbler still gave much smoother hits than a dry piece, but i guess the extra air and water volume of the bong just gives it an edge. I'd imagine however if you got a larger bubbler with a larger chamber the difference would be less noticeable.
The bong was alot easier to clean and maintain. Bubblers are somewhat of a bitch to clean out cause you cant get any kind of tool to scrape out the inside easily. Not a big deal really, just use rubbing alcohol and salt, still does the trick. If you ever smoke resin tho, Its really difficult to collect from bubblers, again not a big deal unless your some sort of resin freak.
The nice thing about bongs is that they have the removable slide bowl. This comes in handy whenever a bowl is finished, cause you can simply flip the bowl upside down, stick it over the slide and suck the ash into the bong water. With bubblers you generally just gotta suck the ash through, because if you try and dump it out your gonna get wet. (If you got a bubbler with a removable slide this would remedy this inconvienience however i dont think they look as cool this way)
All that being said, Id rather have a bubbler over a bong. Their are certain intangible qualities you get with a bubbler. I just like the feel of smoking through a bubbler, your just chilling on your fat waterfiltered pipe. Also, when i smoke alone I generally like to just take small, smooth tokes and just relax with it, Bongs are sorta more involving, and generally work alot better only with big hits. Plus you get the uniqueness factor, everyone and their grandma has a bong, but very few people have bubblers.
Also, If your going glass (the only bubblers ive ever seen are handblown glass) do yourself a favor and dont blow a ton of cash on a super expensive piece. The reason i reffered to my bubbler and bong in the past tense is cause I broke them both