PhD at top department (path - MS (unfunded) to PhD) vs mediocre dept (path - funded PhD) , differences in experience? At the present, I have got MS at Uni A (rank 16 usnews dept grad school)w/o funding for tuition and on the other hand I have a fully-funded PhD offer from uni B (rank 69 usnews dept grad school). At B the research is interesting, the advisor is a great person but the few drawbacks would be that he's relatively new (i'd be his only student in the lab apart from a few UGs, i'm the 2nd PhD), many of his grants are pending, ranking of the dept is relatively low. The reason I didn't apply to PhD programs was due to my avg U-GPA. So, my plan after masters, at least as of now would be to apply to PhD programs (looking at northwestern, upitt, emory, uofchicago, jhu). If I take CWRU, the advisor that I have lined up is willing for me to do independent research, write grant proposals, and work on a number of collaborative projects. 

Can you tell me the main factors to consider when choosing where to do PhD apart from research interest and advisor relationship? I am trying to look at whether this risky choice of MS->PhD (which I am more inclined to) would be better than the PhD offer that I have right now. Risky because i'm not sure if the MS would better my chances at those schools for PhD and if it's worth the 2 years which I could have used for maybe a post-doc after PhD at B. Do top dept's have an edge over relatively lower ranked one's? 

One reason that i'd probably want to do a MS would be to maybe expand my research focus and work under more renowned researchers in the field. Though I could do the same in UH by collaborating with great professors in other dept but would have to work much harder. Any thoughts or inputs?
Comparisons and recommendations of specific universities is off topic here as a "shopping question". I'll restrict this answer to the question of getting an MS first. 

In the US (unlike many other places) getting an MS first isn't necessary and will probably lengthen your total program, especially if you switch programs after the MS. Also, not every MS program will be research focused, though some will. But some are just advanced coursework, even applied coursework if most graduates enter industry. 

If you take the direct PhD path you will probably have an opportunity to get a sort of "freebie" MS along the way, perhaps by doing a small project and writing it up as an MS thesis. 

The main requirements for a doctorate (US) are that you pass a set of comprehensive examinations and that you write an "acceptable" dissertation. There is normally advanced coursework, mostly to prepare for comps. But if you do an MS elsewhere, there is no guarantee that the courses there will give good preparation for comps at the doctoral institution. Maybe they do, maybe not. 

If you can find a good advisor and a good and compatible research program that interests you, I would suggest the direct PhD path over any other. Whether your institution ranks 10 or 110 won't matter nearly as much to your overall career as what you do and what relationships you can develop while studying. And being a top student as the 210th ranked institution is probably better for your career than being a mid-level graduate of the 10th ranked one. At least in obtaining your first job. It is about what you do, not about what others have done to affect rankings. There are good advisors throughout academia. They aren't all at MIT and Berkeley. 



But, there is also the question of the experience of the advisor. I neglected that in the first version here.

The one thing I'd worry about with an inexperienced advisor is where they are in their tenure process. If they are tenured it is not so much of a problem, nor should it be if they are a shoo in. But an advisor who is at risk of not getting tenure may prioritize their own work over helping you. I'd advise against that scenario. 

But if they have a lot of ideas and like to share them, it should otherwise be fine. But look also at the other people in that group. Do they have an effective regular seminar for a few faculty in that field. That is a big plus, again if they share ideas.

I was once "stuck" with an untenured advisor who wasn't helpful.