Is Excel-generated chart acceptable for publication?
Excel can produce high quality charts, but it takes a lot of work. The biggest difference between Excel and other systems is the quality of the defaults. I suspect some people are using excel charts, but they have gone to a lot of effort to tidy them up. 

In the example chart, you will, for example, definitely need to deal with the x-axis labels overlapping the y-grid lines. In fact the y grid lines are too strong - in fact I'd put some more consideration into the gird lines in general - why y lines, but no x lines - there might be a good reason, but you should think about it? 

Limit the y-axis to make 0 the minimum (I'm assuming a negative flux makes no sense). 

I would personally also add a y axis and x-axis border line. You are almost certainly going to want tick marks on the axes. And markers on the lines/larger markers if they are already there but too small. 

Your axis titles need to have the same font size (the y looks bigger than the x to me at the moment) and the difference in font size between the labels and the titles is probably too big. I probably take out half of the x-axis labels and make the remaining ones bigger. 

One thing that Excel is bad with, and isn't easily fixable is consistency. Getting two plots looking exactly the same, with exactly the same size plot, same size text, with all the elements in the same place is really difficult because it relies so much on the mouse and manually moving/sizing things.