A few thoughts about this:
1) Personally, I think it is worth making scientific writing as plain and accurate as possible. If "confounded" indeed describes the relationship between A and B, then that is the term you should use.
2) I don't think "confounded" has a negative connotation at all* - at least in the epidemiology literature. It merely specifies a specific relationship between variables (which you already know.) I'll use the ubiquitous example: in the apparent correlation between alcohol use and heart disease, alcohol use is confounded by smoking status. Not positive, not negative, just descriptive information.
(*Although there's "that paper confounded me!" Or, "that #^~& confounded paper!" But these are different.)
3) Now, you are considering using the term slightly differently, applying it to a whole study rather than variables. But I do not think this shift adds a negative connotation.
Some degree of confounding is ubiquitous; the real issue is the quality of the study. A lousy study can be useless even if there are no major confounders. On the other hand, even if substantial confounding is unavoidable, thoughtful design, skilled implementation, and shrewd analysis can still provide valuable information. So - the presence of confounding alone does not imply any deficiency in the research; nor does it prevent useful study results; I don't perceive any negative connotation.
4) However, my experience is in epidemiology, biostatistics, and medicine - which may or may not be relevant to your thesis. It's difficult to say, without knowing the topic or even the field. Or you may just disagree. So I have another suggestion, in case you decide not to go with "confounded."
A common way to deal with this situation is assign each group an abbreviated or otherwise convenient name, define the names early on (e.g. in the introduction and/or methods section) and use the short names thereafter. Some possibilities:
-Group 1, 2, and 3
-Group A, Group B, and Group AB
-Something more descriptive (e.g. AVS - A variable studies, BVS - B variable studies, and ABVS - A and B variable studies. Personally, I prefer the descriptive abbreviations; otherwise, I too often forget which group is which.)
5) Finally, I agree with checking with your thesis advisor or committee. They may have very specific requirements or preferences. And good luck!