Advancement in science comes from
- repeated (and repeatable) observations that are
- systematically processed,
- hypotheses that get tested on experimental data,
- and conclusions that get peer review.
One high-altitude balloon with low-cost off-the-shelf sensor payload will add nothing to existing space/earth sciences if you do not do the following:
- read principal textbooks on the discipline you want to advance;
- read scientific journals / arXiv papers going back at least 10 years;
- formulate a list of unsolved problems in space/earth sciences;
- choose a few of the problems that can be re-worded into testable hypotheses that need some vertical profile data/high atmospheric measurements;
- verify that your budget allows you to design a data collection campaign with instrument accuracy and number of samples necessary to test the hypotheses;
- document all the decisions you make;
- do Monte Carlo hypothesis testing on mock data;
- calibrate your instrument package against standard sources/instruments (e.g. radiation sources if you are launching a Geiger counter) at the full range of environmental conditions that your balloon will encounter;
- publish the results (arXiv is the best bet here, you'd be well advised to team up with one or two subject matter experts - you can get more info by asking at Academia SE).
As a necessary reminder, you HAVE TO COORDINATE LAUNCH WITH LOCAL AIR CONTROL AUTHORITY.
If you can make the balloon reusable (that is, you can afford going to another country to pick it up or offer an award to any who find it), you stand a much higher chance of getting some stuff done. One vertical profile is unlikely to be useful, though.
After the first couple of papers you can apply for a grant to do more and better stuff without ruining your credit history (unless you are Alfred Lee Loomis or Howard Hughes-rich). No guarantees, but science enjoys economies of scale nowadays.
EDIT: for an insight into cutting-edge real-life high-altitude experiment design, please have a look at this answer at Aviation SE, describing astronomical observations from a Concorde.