I would narrow the considerations to the following questions. (1) is the work potentially useful information for other people to use (i.e., should it be published somewhere because it is _useful_ information), and (2) is the work done in good faith. It seems from your comments that your answer to both those questions is “yes”.
The MDPI journals are peer-reviewed, a repository is not. Moreover, in my experience with peer review, one of the best peer review jobs I had came from an obscure OA journal and one of the poorest peer review jobs I had came from a subscription access (SA) journal. The rest were evenly spread. What you most want is quality feedback from the peer reviewers. Whether OA or SA, you can find reviewers who are politicians or don’t take their job seriously. So, it is the luck of the draw on that.
There is plenty of research that would be good to know, but is difficult to find. Perhaps this is because of the attitudes like insisting that only the thing that are purportedly “new” are worthy of publication in SA journals. It surely encourages people to hype their work with lots of balderdash rather than just write what they did and what they found and let other people decide if it is worth anything. As a researcher, there have been many times that I needed information and could not find it anywhere. Is it because of reasons that you cite, that some editor or reviewer considered it “incremental” or “insignificant”. Should _useful_ research be wasted like that?
It is also important to reflect that research is also sometime the luck of the draw. Sometimes a project turns out to have low lying fruit that quickly yields a publication in PNAS, but it can also be largely a project that yields thistles and thorns even when it seemed like it was a good project at the inception. If the student has the tenacity to stick to the work diligently for 5 years and managed to get something useful from it, it actually may say a lot more about the student than the person who was fortunate enough to catch the low lying fruit the first time. Should the reward go only to those who get lucky and are blessed, or should it also go to those who are persistent and tenacious? Over all, good science is generally the product of persistence and tenacity and lucky breaks are not to be expected in my opinion. You might find the book “Fooled by Randomness” a useful perspective here.
The remaining issue is the journals themselves. Obviously, it is better not to sell yourself short. I don’t know what to recommend here. Career wise, getting lucky the first time opens lots of doors, but a career is a life long journey, and I would say that what is more important is what you actually _do? in that life. I think that it is unfortunate that administrators base their decisions on trivial metrics like impact factor. Some of the greatest works were published in obscure journals, and even Einstein, the icon of great discoveries, published his work at a time when the Annals of Physics did not even have any peer review. Does that make Annals of Physics a “repository”? Work should be judged based on reading the papers, not these false measuring scales.
