So let me see;
1) You do not bootstrap in FastTree - you bootstrap in seqboot and consense from Phylip as FastTree has no bootstrap function built in. So if we are playing pedantry I am right and Editor 2 is wrong. Why do I want to know the variation under an approximate method? It was created for large sequence trees for speed not accuracy. The key to the paper is identifying if the H5N8 hemagglutinin and neuraminidase genes are part of a single cluster or multiple clusters. The bootstrap tells you NOTHING about this because it just tells you the variability of the method nothing about the biology and the results. These same multiple clusters are identified in both the neuraminidase and hemagglutinin trees. These are independent samples as opposed to covariate sites tested in a bootstrap and so if they agree it is very unlikely the trees are wrong. Bootstraps add nothing other than a sop to the phylogenetics community who cannot live without them.
2) I explained the methods - they both use ML GTR + gamma + I just in different programs FastTree for the big alignment and Mega for the small alignments. Editor 2 had actually told me to use FastTree in a previous paper where these H5 and N8 trees were needed as supplementary data. In that case it was to confirm my Bayesian tree did not have recombinations, it was in doing that, that I found the result reported here. So I am quite stunned that he has forgotten that this is the method he actually suggested.
3) The figures are vector graphics - is it beyond the wit of an editor to zoom a figure. Even if they are in need of editing THIS IS NEVER A REASON FOR REJECTING A PAPER for revisions yes but rejection you have to be joking. Each tip is labelled in that way because the BIOLOGY is what matters i.e. the location and date of the sequences were I to shorten to database identity this would make interpreting the trees impossible in terms of biology and it would also be impossible to see that the trees show a coherent pattern in terms of date and location. The problem is we get so carried away with algorithms we no longer look at the data. If a cluster is all from New Jersey in 1989 then that is a reasonable cluster in good agreement with geography and chronology.
4) I object to the word sloppily. It is not a term that should ever enter an editor's response. You may say the paper is missing a reference at point A and point B but sloppily is pure hyperbole and not worthy of a good editor. It is not a word I would ever use. Still more it is not justification for more than major revisions.
I have been an editor for 4 years and edited 120 papers and I would never write such a response or make such a decision without proper justification especially given the final part about it being mostly technically correct. Not being presented in a way that is a useful contribution is NOT a CRITERIA for rejection, at most it is for Major revision especially at initial submission. We do not judge on significance we judge on it being SCIENCE.