Stating that my research hold less value compared to another topic. A good idea? In a couple of days I have to present my master's thesis, which is on a topic of Information System (IS) implementation in a small organisation.

I conduct a study of critical success factors, but during my research I found that the organisation has deeper problems like readiness, culture and knowledge gaps. Therefore, I think that a study on these aspects would give them more value.

Do you think that I should mention this during my research presentation?

Thanks for your time.
Your research doesn't have less value simply because you uncovered problems broader than (or different from) what you chose to focus on. An equal way of stating the outcome is to say that your work has opened a door to at least one promising additional line of research! We as researchers are facing the unknown; we necessarily do not know what the results are going to look like ahead of time. Scientifically speaking, as long as the study is well-supported and well-designed, an unexpected outcome is precisely as valuable as a result that looks as expected and/or upholds a hypothesis.

Your presentation will be better if it is self-assured. Confidently and straightforwardly, lay out what you did and how you went about it and what you have discovered, and put in a few slides at the end conveying some excitement about the potential inherent in the interesting things that your work is pointing the way towards. Every study has limitations, and good scientific practice is to acknowledge these transparently but not apologetically. No study can do everything. Knowledge is a collaborative effort, and we can build on each other's findings if we have a good sense of what has been done how.

My MA thesis, in retrospect, had a lot of things in it that I now know to have been oversimplifications. I didn't have a full sense of what was going on; there was so much more to it than that! But I couldn't have gotten here from there. A master's thesis is often a stepping-stone; I'd say that's both natural and usually inevitable. If you feel as if there are signs of you needing to look beyond the scope of a master's paper - I spotted some in mine as well! - that's what I'd call a sign that you're ready for a Ph.D. (if that is your aim).