Note: The below refers entirely to moving between QV and the installed version of QS. Quite possibly some of these things would not apply if moving to SaaS.
I found the biggest challenge to be fitting everything on the screen. QS is responsive, which is great in some ways but very frustrating in others, and the text tends to be much larger than in QV apps, so I simply wasn't able to fit as many things in as I was on a QV canvas. Another major issue is that Qlik Sense pivot tables are completely unsatisfactory - we ended up using a third party extension - and do not allow expand/collapse to a specific dimension level or a preset expand/collapse level.
Other issues, in no particular order:
1) Inferior export-to-excel options
2) Lack of cyclic groups that work across all objects (but workarounds are available)
3) Harder to control which users see which apps (in QV this was automatic based on section access, in QS it is not)
4) Clunky development process since you can't just open a file and start messing around (often without saving)
5) QS hub isn't great, can't mark favorite apps to view in one place is an issue that was particularly commented on by our users
Not to make everything sound negative, there were of course many advantages as well - master items are a blessing compared to copying formulas to each object individually, the reload scheduling is much better than QV, Insights can be quite helpful in some contexts, responsiveness is an advantage any time it doesn't break your objects, Alternatives are in many cases better than cyclic groups, Selections and Smart Search are brilliant, and so on.
We did not have any major technical issues that I recall offhand.
I think the things to know would largely depend on your existing environment and QVWs, and how you plan to approach the project insofar as "Copy as much as you can over with minimal changes" vs "Rethink our apps in the context of Qlik Sense". For the former, I would say re-planning your canvas real estate and pivot tables may well be the biggest challenges. For the latter, it's just getting everyone on the correct page insofar as QS simply being different from QV.
