What does it mean when a paper is rejected but encourages resubmission without a suggestion of new experiments? My paper has been rejected but encouraged re-submission. The reviewers were overall positive said it was well written and that all the analyses were correct. The problems pointed out were changes to the introduction and conclusion to change the scope of how the experiments are framed, not to any of the experiments themselves. There were no mentions of lack of novelty or other common reasons for rejection. There was also no mention that anything I wrote was overstated or incorrect.

I am unsure of whether to  re-submit when it has been rejected for this reason because I don't understand how a manuscript could be rejected if the experiments were correct and found to be novel? 
If the problem is that I need to modify my introduction and conclusion than why not accept the manuscript, since re-writing the introduction/conclusion would not be very difficult. I would consider doing so would be a minor revision.

I am wondering whether anyone has had this type of rejection before and if they decided to re-submit or submit elsewhere?
Many journals are now encouraged to publish the data on the "efficiency" of the review process, e.g. the average time before initial submission and publication. Expected time to publication may be an important consideration for authors, along with the journals impact factor. 

So, imagine that you run a journal, where a paper on average goes through 2.5 rounds of review and each round takes 3-6 months. If you sum it together, 12+ months from submission to publication would not look too attractive. But you only need to sum up if you invite revisions. If you "reject and resubmit", then technically you look at a completely new submission, and it counts as a new paper in your statistics. So, your processing rate gets shorter (which authors like), and your acceptance rate gets lower (which makes your journal sort of a prestigious one, tough to get into). 

This is the main reason (in my personal opinion), why so many journals now rebrand "major revision" decision (and often "minor revision" as well) as "reject and resubmit".