I did the whole grad school application dance a couple years back. It sucked. No, scratch that. It really sucked.
You’re right about the MS/PhD decision. There is almost no funding for MS students at most places. You’re basically there to add to the bottom line, whereas the PhD students are there to add to the schools publication record and future bragging rights. 3 guesses as to who gets funded.
Things vary from school to school, but in general the overwhelming thing they look at in phd-admits is evidence of potential for research. Your intern experiences may or may not show this, depending on what you did. Par for the course is usually a solid senior thesis, and even better is a senior thesis that got a publication somewhere. They do cut a fair amount of slack if you went to a school where that was difficult, i.e. small liberal arts schools and whatnot. Woe upon you if you went to a big research school and did no research as an undergrad. Grades, GREs, etc are usually things that determine if you get rejected rather than things that get you in.
A fair number of schools will seperate the PhD admits and the MS admits into a caste system. Occasionally, getting admited as an MS student is basically the kiss of death to applying to the PhD program. I dont know of any BME programs that are run this way, but its not unheard of.
If you have the chance, visit all the places that you got accepted to. Key things to look for: are the grad students happy? Whats the area like? Ask about how you get an advisor. If you go someplace with exactly one big name, then there’s usually a feeding frenzy to become their student. It’s rarely a positive experience. Will you have dental insurance or will the only affordable dental care drive up to campus in a van? (past pet peeve)
Also, ask (current grad students, not the shiny happy admissions people they have you talk to) how many years of hazing do you get? In most programs you get absolutely worked your first year. Some places, its two. Legend has it, some schools actually treat you pretty well your first year, but these tend to be a royal bitch to get into. Qual pass rates are also a factor, in general avoid places that throw you in with a couple hundred other people and make you take a qual with a 30% pass rate to get into the phd program.
So, yeah. Have, uh, fun. Yes, thats it. Fun.
http://www.phdcomics.com is a snarky look at grad student life, though you may want to hold off so you dont get prematurely jaded.