The main reason, I think, that people are having issues with the bridge location fall into three categories.
1) Being there, right in the flight path of landing shuttles (assuming that the fwd bay is for landings as well as takeoffs... which isn't the case on aircraft carriers today, for instance!), is a bit risky.
2) It's just not very identifiable from outside.
3) It's not where people are used to seeing it.
I think that the first one might be a legitimate complaint... and, of course, it's my OWN sole "complaint" about that location.
The second one is easy to fix. Just some more prominent features there to make it visible. Perhaps it's protruding slightly (see the big cargo plane image from a few posts back again)?
One more possible concern... the bay doors are on a rail, and need to be sealed... is there sufficient space above the "bridge" area to allow for the mechanical components required to operate (and seal, don't forget!) the door?
The third one is nonsense, of course, but is probaby the most common complaint. There's NOTHING wrong with breaking "style-only" design rules, and giving people something that they're not used to seeing.
Just FYI, if it were ME doing this design, I might put the bridge in the forward quarter-spherical element of the underbody structure (the stuff you originally had down there, I mean. That gives you plenty of separation between the bridge and the landing deck (with all its noise and activity), still gives you a "forward, semi-exposed" placement (though on the bottom, not the top, as people seem to expect!) and so forth.
Just a suggestion.