Rather than listing the differences between a PhD and Masters, we will assume scenarios to discuss the qualitative and future implication of the degree on a career.
BACKGROUND: At most institutions, Masters is limited to 2 years and has less stringent requirements to graduate. Masters degree would not expect you to publish a research article; whereas it is a requirement in PhD at many institutions. So when would you choose one over the other?
Love science and wanted to be a scientist since you were a kid:
No good reason why you shouldn’t do a PhD. Even if you decide to do science in the industry, PhD would be an asset. But an internship would be a good starter before getting started with grad school to help you make better choices (which lab, which project, etc).
Love science but not sure research is for you:
The only way to know is if you try. Do an internship. If this is not an option, Masters is shorter than PhD. To be exact, Masters has a built-in time limit of 2 years (usually in North America). PhD has a longer time limit from 4-7 years. PhD can be done in 2 years, but you WILL finish a Masters in 2 years. During your Masters you can find out if you want to do more scientific research with PhD or find an alternate path; either into scientific industry or an alternate field. Masters provides flexibility.
One might ask: then why not always start with a Masters? In fact, Masters is a requirement before entrance to PhD in many European countries. The only down-side to doing a Masters is you might spend a bit more time with student wage (Masters 2 years + PhD 3-5 years vs. PhD 3-5 years).
Love science but do not want to be an academic scientist:
*Definition of an academic scientist = someone who acquires grants/funding and does scientific research for a living.
Masters would provide you with quick insight of scientific research which can help you in non-academic path you will follow. Let’s consider an example where one would have a career in pharmaceutical industry. Masters, compared to an undergraduate degree, would help your career. Very little doubt here. PhD, however, is not a clear cut answer. Some people who has been in the pharmaceutical industry for many years advised that there is a ceiling that would be hard to surpass without a PhD. Whereas, many opinions regarding getting a position with a PhD is harder due to minimum wage of a PhD is higher, and the companies sometimes prefer to hire a Masters. In this scenario, best judgement will come from which career one wants to pursue afterwards.
When PhD is the best choice:
If you want to become an academic scientists, do a PhD. Even if you are pursuing an MD (for those who want to do clinically oriented research), doing an MD/PhD would be prudent considering how competitive it is getting to acquire a P. I. position. Few principle investigator (academic scientist) will lack a PhD or similar certificate in the near future.
When neither PhD or Masters is viable choice:
If you did a bachelors (or equivalent) in science and science does not seem that interesting; research is not for you. Research is difficult. Difficult because scientific research is the forefront of human knowledge. At this fringe, many things are not clear-cut and educated guess must be made and many of these guesses will be wrong. It is tough when your hard work shouts in your face you are wrong so liking science itself is a pre-requisite.
Capital ‘T’ truth here is: try research and do graduate scientific research only if you find science fascinating.