Here are the obvious ones I've seen so far in reading through the report.
For the EU: The finding that certain launch aid/member State financing constitutes prohibited export subsidies (paras. 7.582-716). It would be nice for the EU to not have these subsidies classified as "prohibited" (although implementation may not be all that difficult).
For the U.S.: Launch aid/member State financing is not a program (paras. 7.498-581). The U.S. would be in a much better position to stop future (alleged) subsidies if they could get a finding that the program itself constitutes a prohibited export subsidy.
The appeal problem with both of these issues is that, in my view, they were very close calls (note that this is based on one read-through of each). There was not a clear cut finding to be made one way or the other, nor were there any glaring errors in the panel's findings. Also, both findings were fact-intensive, which can make appeals difficult. The parties might have to go into DSU Article 11, which is not always a place you want to go.
Also of interest was this statement by the panel: "7.675 In our view, a government's motivation for granting a particular subsidy, to the extent it can be established from the evidence and arguments presented by the parties in dispute, will be highly relevant when evaluating whether a subsidy has been granted contingent in fact upon export performance within the meaning of Article 3.1(a) of the SCM Agreement. ..." As I've mentioned before, I like intent, but I don't think most people like it is as much as I do, so I'll be curious what the Appellate Body says about this.